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Jaccard_index
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LUYAO REN 5 jaren geleden
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      codescript/.DS_Store
  2. +33
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      codescript/lcl5filelist
  3. +73
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      codescript/rtg_pairs.py
  4. +192
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      codescript/rtg_pairs.txt
  5. +11
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      inputs
  6. +29
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      tasks/jaccard_index.wdl
  7. +26
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      tasks/mergeJI.wdl
  8. +25
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      tasks/prepare_pairs.wdl
  9. +47
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      workflow.wdl

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codescript/.DS_Store Bestand weergeven


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codescript/lcl5filelist Bestand weergeven

oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz

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codescript/rtg_pairs.py Bestand weergeven

import itertools
import pandas as pd
import sys,argparse,os

parser = argparse.ArgumentParser(description="this script is to preform combination on vcf files, get any two of them for next jaccard index calculation")

parser.add_argument('-vcf', '--vcffile', type=str, help='input vcf file', required=True)

args = parser.parse_args()

# Rename input:
vcf_input = args.vcffile


file = pd.read_csv(vcf_input,header=None,sep='\t')
com = list(itertools.combinations(file[0],2))

outfile = open('rtg_pairs.txt','w')

for pair in com:
# prepare a
one = pair[0].strip().split('/')
a = one[len(one)-1].replace('.normed.vcf.gz','')
strings_a = a.strip().split('_')
sequenceTechA = strings_a[0] + strings_a[1]
sequenceSiteA = strings_a[2]
sampleA = strings_a[3]
repA = strings_a[4]
# analysisSiteA = strings_a[8]
# pipelineA = strings_a[9] + strings_a[10]

# prepare b
two = pair[1].strip().split('/')
b = two[len(two)-1].replace('.normed.vcf.gz','')
strings_b = b.strip().split('_')
sequenceTechB = strings_b[0] + strings_b[1]
sequenceSiteB = strings_b[2]
sampleB = strings_b[3]
repB = strings_b[4]
# analysisSiteB = strings_b[8]
# pipelineB = strings_b[9] + strings_b[10]

folder = a + '-' + b
## add annotation
# sequencing technology
if (sequenceTechA != sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB):
outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'sequenceTech' + '\n'
outfile.write(outline)
# sequencing site
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA != sequenceSiteB) and (sampleA == sampleB):
outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'sequenceSite' + '\n'
outfile.write(outline)
# sample
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA != sampleB):
outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'Sample' + '\n'
outfile.write(outline)
# replicate
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB) and (repA != repB):
outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'replicate' + '\n'
outfile.write(outline)
# analysis site
# elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB):
# outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'analysisSite' + '\n'
# outfile.write(outline)
# pipeline
# elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB) and (analysisSiteA == analysisSiteB) and (pipelineA != pipelineB):
# outline = pair[0] + '\t' + pair[1] + '\t' + folder + '\t' + 'pipeline' + '\n'
# outfile.write(outline)
else:
pass

outfile.close()


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codescript/rtg_pairs.txt Bestand weergeven

oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_BGI_LCL5_2_20180530 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_BGI_LCL5_3_20180530 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_BGI_LCL5_3_20180530 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402-BGI_SEQ2000_WGE_LCL5_2_20190402 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328-BGI_SEQ500_BGI_LCL5_2_20180328 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328-BGI_SEQ500_BGI_LCL5_3_20180328 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328-BGI_SEQ500_BGI_LCL5_3_20180328 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_2_20181108 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_3_20181108 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_3_20181108 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
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oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
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oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_ARD_LCL5_5_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_ARD_LCL5_6_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_ARD_LCL5_6_20190111 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
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oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
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oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_BRG_LCL5_2_20180930 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_BRG_LCL5_3_20180930 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_BRG_LCL5_2_20180930 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_BRG_LCL5_3_20180930 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_BRG_LCL5_3_20180930 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_1_20170329 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_2_20170329 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_3_20170329 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_1_20170216 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_2_20170216 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_3_20170216 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_4_20180703 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_5_20180703 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_6_20180703 sequenceTech
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_ARD_LCL5_2_20170403 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_ARD_LCL5_3_20170403 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_ARD_LCL5_3_20170403 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_NVG_LCL5_2_20170329 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_NVG_LCL5_3_20170329 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_NVG_LCL5_3_20170329 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_2_20170216 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_3_20170216 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_3_20170216 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703-ILM_XTen_WUX_LCL5_5_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703-ILM_XTen_WUX_LCL5_6_20180703 replicate
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703-ILM_XTen_WUX_LCL5_6_20180703 replicate

+ 11
- 0
inputs Bestand weergeven

{
"{{ project_name }}.pairs.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg_pairs:v1.0",
"{{ project_name }}.vcf_dir": "{{ vcf_dir }}",
"{{ project_name }}.disk_size": "100",
"{{ project_name }}.mergeJI.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
"{{ project_name }}.JI.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
"{{ project_name }}.bed": "{{ bed }}",
"{{ project_name }}.sdf": "oss://chinese-quartet/quartet-storage-data/reference_data/GRCh38.d1.vd1.sdf/",
"{{ project_name }}.filelist": "{{ filelist }}",
"{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.xlarge img-ubuntu-vpc"
}

+ 29
- 0
tasks/jaccard_index.wdl Bestand weergeven

task JI {
File vcf_a
File vcf_b
File dir_name
File sdf
File bed
File vcf_dir
String docker
String cluster_config
String disk_size
command <<<
set -o pipefail
set -e

/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${vcf_a} -c ${vcf_b} -o ${dir_name} -t ${sdf} --bed-regions=${bed}

>>>

runtime {
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File JI_summary = "${dir_name}/summary.txt"
}
}

+ 26
- 0
tasks/mergeJI.wdl Bestand weergeven

task mergeJI {
Array[File] JI_summary
File inputJIpiarsFile
String docker
String cluster_config
String disk_size
command <<<
touch number
for i in ${sep=" " JI_summary}
do
cat $i | sed -n '4,4p' | sed 's/\s\+/\t/g'| cut -f4-6 >> number
done
paste ${inputJIpiarsFile} number > result.txt
>>>

runtime {
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File JI_all = "result.txt"
}
}

+ 25
- 0
tasks/prepare_pairs.wdl Bestand weergeven

task pairs {
File filelist
File vcf_dir
String docker
String cluster_config
String disk_size
command <<<
set -o pipefail
set -e

python /opt/rtg_pairs.py -vcf ${filelist}

>>>

runtime {
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File rtg_pairs = "rtg_pairs.txt"
}
}

+ 47
- 0
workflow.wdl Bestand weergeven

import "./tasks/prepare_pairs.wdl" as pairs
import "./tasks/jaccard_index.wdl" as JI
import "./tasks/mergeJI.wdl" as mergeJI


workflow {{ project_name }} {

File filelist
File vcf_dir
File sdf
File bed
String cluster_config
String disk_size

call pairs.pairs as pairs {
input:
filelist=filelist,
cluster_config=cluster_config,
disk_size=disk_size
}

Array[Array[File]] inputJIpairs = read_tsv(pairs.rtg_pairs)

scatter (pair in inputJIpairs) {
call JI.JI as JI {
input:
vcf_a=pair[0],
vcf_b=pair[1],
dir_name=pair[2],
vcf_dir=vcf_dir,
bed=bed,
sdf=sdf,
cluster_config=cluster_config,
disk_size=disk_size
}
}

call mergeJI.mergeJI as mergeJI {
input:
JI_summary=JI.JI_summary,
inputJIpiarsFile=pairs.rtg_pairs,
cluster_config=cluster_config,
disk_size=disk_size
}

}


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