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replicate ji

master
LUYAO REN 1 year ago
parent
commit
f881e4fce1
7 changed files with 109 additions and 286 deletions
  1. +0
    -33
      codescript/lcl5filelist
  2. +33
    -0
      codescript/lcl5filelist.txt
  3. +21
    -47
      codescript/rtg_pairs.py
  4. +48
    -192
      codescript/rtg_pairs.txt
  5. +3
    -5
      inputs
  6. +3
    -4
      tasks/jaccard_index.wdl
  7. +1
    -5
      workflow.wdl

+ 0
- 33
codescript/lcl5filelist View File

@@ -1,33 +0,0 @@
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

+ 33
- 0
codescript/lcl5filelist.txt View File

@@ -0,0 +1,33 @@
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_2_20190402
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703
oss://pgx-result/renluyao/high_confidence_call/LCL5/VCF/ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703

+ 21
- 47
codescript/rtg_pairs.py View File

@@ -2,7 +2,7 @@ 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 = argparse.ArgumentParser(description="this script is to preform combination on vcf files, get any two of three replicates for next jaccard index calculation")

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

@@ -13,61 +13,35 @@ vcf_input = args.vcffile


file = pd.read_csv(vcf_input,header=None,sep='\t')
com = list(itertools.combinations(file[0],2))
location_com = list(itertools.combinations(file[0],2))
name_com = list(itertools.combinations(file[1],2))
num = len(name_com)

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

for pair in com:
for i in range(0,num):
# prepare a
one = pair[0].strip().split('/')
file_a = one[len(one)-1]
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]
one = name_com[i][0]
strings_one = one.split('_')
sequenceTechA = strings_one[0] + strings_one[1]
sequenceSiteA = strings_one[2]
sampleA = strings_one[3]
repA = strings_one[4]

# prepare b
two = pair[1].strip().split('/')
file_b = two[len(two)-1]
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
two = name_com[i][1]
strings_two = two.split('_')
sequenceTechB = strings_two[0] + strings_two[1]
sequenceSiteB = strings_two[2]
sampleB = strings_two[3]
repB = strings_two[4]

folder = one + '-' + two
## add annotation
# sequencing technology
if (sequenceTechA != sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB):
outline = file_a + '\t' + file_b + '\t' + folder + '\t' + 'sequenceTech' + '\n'
outfile.write(outline)
# sequencing site
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA != sequenceSiteB) and (sampleA == sampleB):
outline = file_a + '\t' + file_b + '\t' + folder + '\t' + 'sequenceSite' + '\n'
outfile.write(outline)
# sample
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA != sampleB):
outline = file_a + '\t' + file_b + '\t' + folder + '\t' + 'Sample' + '\n'
outfile.write(outline)
# replicate
elif (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB) and (repA != repB):
outline = file_a + '\t' + file_b + '\t' + folder + '\t' + 'replicate' + '\n'
if (sequenceTechA == sequenceTechB) and (sequenceSiteA == sequenceSiteB) and (sampleA == sampleB) and (repA != repB):
outline = location_com[i][0] + '\t' + location_com[i][1] + '\t' + folder + '\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


+ 48
- 192
codescript/rtg_pairs.txt View File

@@ -1,192 +1,48 @@
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_BGI_LCL5_2_20180530 replicate
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_BGI_LCL5_3_20180530 replicate
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_1_20180518.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_BGI_LCL5_3_20180530 replicate
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_2_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_2_20180530-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ2000_WGE_LCL5_1_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ2000_WGE_LCL5_2_20190402 sequenceSite
BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_1_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_2_20180328 sequenceTech
BGI_SEQ2000_BGI_LCL5_3_20180530.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_3_20180530-BGI_SEQ500_BGI_LCL5_3_20180328 sequenceTech
BGI_SEQ2000_WGE_LCL5_1_20190402.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_2_20190402.normed.vcf.gz BGI_SEQ2000_WGE_LCL5_1_20190402-BGI_SEQ2000_WGE_LCL5_2_20190402 replicate
BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328-BGI_SEQ500_BGI_LCL5_2_20180328 replicate
BGI_SEQ500_BGI_LCL5_1_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_1_20180328-BGI_SEQ500_BGI_LCL5_3_20180328 replicate
BGI_SEQ500_BGI_LCL5_2_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_3_20180328.normed.vcf.gz BGI_SEQ500_BGI_LCL5_2_20180328-BGI_SEQ500_BGI_LCL5_3_20180328 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_2_20181108 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_3_20181108 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_1_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_1_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_3_20181108 replicate
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_2_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_2_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_4_20190111 replicate
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_5_20190111 replicate
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_ARD_LCL5_6_20190111 replicate
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_3_20181108.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_3_20181108-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_ARD_LCL5_5_20190111 replicate
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_ARD_LCL5_6_20190111 replicate
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_4_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_4_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_ARD_LCL5_6_20190111 replicate
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_5_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_5_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_1_20180930 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_2_20180930 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_BRG_LCL5_3_20180930 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_1_20170403 sequenceTech
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_2_20170403 sequenceTech
ILM_Nova_ARD_LCL5_6_20190111.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_Nova_ARD_LCL5_6_20190111-ILM_XTen_ARD_LCL5_3_20170403 sequenceTech
ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_BRG_LCL5_2_20180930 replicate
ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_BRG_LCL5_3_20180930 replicate
ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20171024-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_BRG_LCL5_2_20180930 replicate
ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_BRG_LCL5_3_20180930 replicate
ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_1_20180930.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_1_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_BRG_LCL5_3_20180930 replicate
ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_2_20180930.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_2_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_GAC_LCL5_1_20171025 sequenceSite
ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_BRG_LCL5_3_20180930.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_BRG_LCL5_3_20180930-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025-ILM_Nova_NVG_LCL5_1_20171024 sequenceSite
ILM_Nova_GAC_LCL5_1_20171025.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_GAC_LCL5_1_20171025-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_Nova_WUX_LCL5_1_20171024 sequenceSite
ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_1_20170329 sequenceTech
ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_2_20170329 sequenceTech
ILM_Nova_NVG_LCL5_1_20171024.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_Nova_NVG_LCL5_1_20171024-ILM_XTen_NVG_LCL5_3_20170329 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_1_20170216 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_2_20170216 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_3_20170216 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_4_20180703 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_5_20180703 sequenceTech
ILM_Nova_WUX_LCL5_1_20171024.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_Nova_WUX_LCL5_1_20171024-ILM_XTen_WUX_LCL5_6_20180703 sequenceTech
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_ARD_LCL5_2_20170403 replicate
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_ARD_LCL5_3_20170403 replicate
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_ARD_LCL5_1_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_1_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_ARD_LCL5_3_20170403 replicate
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_ARD_LCL5_2_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_2_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_1_20170329 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_2_20170329 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_NVG_LCL5_3_20170329 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_ARD_LCL5_3_20170403.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_ARD_LCL5_3_20170403-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_NVG_LCL5_2_20170329 replicate
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_NVG_LCL5_3_20170329 replicate
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_NVG_LCL5_1_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_1_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_NVG_LCL5_3_20170329 replicate
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_NVG_LCL5_2_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_2_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_1_20170216 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_2_20170216 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_3_20170216 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_4_20180703 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_5_20180703 sequenceSite
ILM_XTen_NVG_LCL5_3_20170329.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_NVG_LCL5_3_20170329-ILM_XTen_WUX_LCL5_6_20180703 sequenceSite
ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_2_20170216 replicate
ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_3_20170216 replicate
ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
ILM_XTen_WUX_LCL5_1_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_1_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_3_20170216 replicate
ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
ILM_XTen_WUX_LCL5_2_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_2_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_4_20180703 replicate
ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_5_20180703 replicate
ILM_XTen_WUX_LCL5_3_20170216.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_3_20170216-ILM_XTen_WUX_LCL5_6_20180703 replicate
ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703-ILM_XTen_WUX_LCL5_5_20180703 replicate
ILM_XTen_WUX_LCL5_4_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_4_20180703-ILM_XTen_WUX_LCL5_6_20180703 replicate
ILM_XTen_WUX_LCL5_5_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_6_20180703.normed.vcf.gz ILM_XTen_WUX_LCL5_5_20180703-ILM_XTen_WUX_LCL5_6_20180703 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_2_20180530.normed.vcf.gz BGI_SEQ2000_BGI_LCL5_1_20180518-BGI_SEQ2000_BGI_LCL5_2_20180530
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

+ 3
- 5
inputs View File

@@ -1,11 +1,9 @@
{
"{{ 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 }}.pairs.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/quality_control:v1.0",
"{{ 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 }}.JI.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
"{{ 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"
}
}

+ 3
- 4
tasks/jaccard_index.wdl View File

@@ -3,8 +3,6 @@ task JI {
String vcf_b
String dir_name
File sdf
File bed
File vcf_dir
String docker
String cluster_config
String disk_size
@@ -13,7 +11,8 @@ task JI {
set -o pipefail
set -e

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

>>>

@@ -24,6 +23,6 @@ task JI {
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File JI_summary = "${dir_name}/summary.txt"
File JI_summary = "${dir_name}.txt"
}
}

+ 1
- 5
workflow.wdl View File

@@ -3,12 +3,10 @@ import "./tasks/jaccard_index.wdl" as JI
import "./tasks/mergeJI.wdl" as mergeJI


workflow {{ project_name }} {
workflow project_name {

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

@@ -27,8 +25,6 @@ workflow {{ project_name }} {
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

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