intergration process

codescripts/high_confidence_call_vote.py

+# import modules
+import sys, argparse, os
+import fileinput
+import re
+import pandas as pd
+from operator import itemgetter
+from collections import Counter
+from itertools import islice  
+
+# input arguments
+parser = argparse.ArgumentParser(description="this script is to count voting number")
+
+parser.add_argument('-vcf', '--multi_sample_vcf', type=str, help='The VCF file you want to count the voting number',  required=True)
+parser.add_argument('-dup', '--dup_list', type=str, help='Duplication list',  required=True)
+parser.add_argument('-sample', '--sample_name', type=str, help='which sample of quartet',  required=True)
+parser.add_argument('-prefix', '--prefix', type=str, help='Prefix of output file name',  required=True)
+
+args = parser.parse_args()
+multi_sample_vcf = args.multi_sample_vcf
+dup_list = args.dup_list
+prefix = args.prefix
+sample_name = args.sample_name
+
+vcf_header = '''##fileformat=VCFv4.2
+##fileDate=20191224
+##source=high_confidence_calls_intergration(choppy app)
+##reference=GRCh38.d1.vd1
+##INFO=<ID=PCT,Number=1,Type=Float,Description="Percentage of votes">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=TWINS,Number=0,Type=Flag,Description="0 for sister consistent, 1 for sister inconsistent">
+##FORMAT=<ID=TRIO5,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
+##FORMAT=<ID=TRIO6,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
+##contig=<ID=chr1,length=248956422>
+##contig=<ID=chr2,length=242193529>
+##contig=<ID=chr3,length=198295559>
+##contig=<ID=chr4,length=190214555>
+##contig=<ID=chr5,length=181538259>
+##contig=<ID=chr6,length=170805979>
+##contig=<ID=chr7,length=159345973>
+##contig=<ID=chr8,length=145138636>
+##contig=<ID=chr9,length=138394717>
+##contig=<ID=chr10,length=133797422>
+##contig=<ID=chr11,length=135086622>
+##contig=<ID=chr12,length=133275309>
+##contig=<ID=chr13,length=114364328>
+##contig=<ID=chr14,length=107043718>
+##contig=<ID=chr15,length=101991189>
+##contig=<ID=chr16,length=90338345>
+##contig=<ID=chr17,length=83257441>
+##contig=<ID=chr18,length=80373285>
+##contig=<ID=chr19,length=58617616>
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr22,length=50818468>
+##contig=<ID=chrX,length=156040895>
+'''
+
+# read in duplication list
+dup = pd.read_table(dup_list,header=None)
+var_dup = dup[0].tolist()
+
+# output file
+file_name = prefix + '_annotated.vcf'
+outfile = open(file_name,'w')
+
+# write VCF
+outputcolumn = '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tQuartet_DNA_BGI_SEQ2000_BGI_1_20180518_LCL5\tQuartet_DNA_BGI_SEQ2000_BGI_2_20180530_LCL5\tQuartet_DNA_BGI_SEQ2000_BGI_3_20180530_LCL5\tQuartet_DNA_BGI_SEQ2000_WGE_1_20190402_LCL5\tQuartet_DNA_BGI_SEQ2000_WGE_2_20190402_LCL5\tQuartet_DNA_BGI_SEQ500_BGI_1_20180328_LCL5 \tQuartet_DNA_BGI_SEQ500_BGI_2_20180328_LCL5\tQuartet_DNA_BGI_SEQ500_BGI_3_20180328_LCL5\tQuartet_DNA_ILM_Nova_ARD_1_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_2_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_3_20181108_LCL5\tQuartet_DNA_ILM_Nova_ARD_4_20190111_LCL5\tQuartet_DNA_ILM_Nova_ARD_5_20190111_LCL5\tQuartet_DNA_ILM_Nova_ARD_6_20190111_LCL5\tQuartet_DNA_ILM_Nova_BRG_1_20171024_LCL5\tQuartet_DNA_ILM_Nova_BRG_1_20180930_LCL5\tQuartet_DNA_ILM_Nova_BRG_2_20180930_LCL5\tQuartet_DNA_ILM_Nova_BRG_3_20180930_LCL5\tQuartet_DNA_ILM_Nova_GAC_1_20171025_LCL5\tQuartet_DNA_ILM_Nova_NVG_1_20171024_LCL5\tQuartet_DNA_ILM_Nova_WUX_1_20171024_LCL5\tQuartet_DNA_ILM_XTen_ARD_1_20170403_LCL5\tQuartet_DNA_ILM_XTen_ARD_2_20170403_LCL5\tQuartet_DNA_ILM_XTen_ARD_3_20170403_LCL5\tQuartet_DNA_ILM_XTen_NVG_1_20170329_LCL5\tQuartet_DNA_ILM_XTen_NVG_2_20170329_LCL5\tQuartet_DNA_ILM_XTen_NVG_3_20170329_LCL5\tQuartet_DNA_ILM_XTen_WUX_1_20170216_LCL5\tQuartet_DNA_ILM_XTen_WUX_2_20170216_LCL5\tQuartet_DNA_ILM_XTen_WUX_3_20170216_LCL5\tQuartet_DNA_ILM_XTen_WUX_4_20180703_LCL5\tQuartet_DNA_ILM_XTen_WUX_5_20180703_LCL5\tQuartet_DNA_ILM_XTen_WUX_6_20180703_LCL5' +'\t'+ sample_name+'_pcr'+'\t' + sample_name+'_pcr-free'+ '\t'+ sample_name +'consensus' + '\n'
+outfile.write(vcf_header)
+outfile.write(outputcolumn)
+
+#function
+def vote_percentage(strings):
+	strings = [x.replace('0/0','.') for x in strings]
+	gt = [x.split(':')[0] for x in strings]
+	percentage = round((33 - gt.count('.'))/33,2)
+	return(str(percentage))
+
+def decide_by_rep(strings):
+	consensus_rep = ''
+	mendelian = [x[-5:] for x in strings]
+	strings = [x.replace('.','0/0') for x in strings]
+	gt = [x.split(':')[0] for x in strings]
+	# mendelian consistent?
+	mendelian_dict = Counter(mendelian)
+	highest_mendelian = mendelian_dict.most_common(1)
+	candidate_mendelian = highest_mendelian[0][0]
+	freq_mendelian = highest_mendelian[0][1]
+	if (candidate_mendelian == '1:1:1') and (freq_mendelian >= 2):
+		gt_num_dict = Counter(gt)
+		highest_gt = gt_num_dict.most_common(1)
+		candidate_gt = highest_gt[0][0]
+		freq_gt = highest_gt[0][1]
+		if (candidate_gt != '0/0') and (freq_gt >= 2):
+			consensus_rep = candidate_gt
+		elif (candidate_gt == '0/0') and (freq_gt >= 2):
+			consensus_rep = '0/0'
+		else:
+			consensus_rep = 'inconGT'
+	elif (candidate_mendelian == '.') and (freq_mendelian >= 2):
+		consensus_rep = 'noInfo'
+	else:
+		consensus_rep = 'inconMen'
+	return consensus_rep
+
+
+def main():
+	for line in fileinput.input(multi_sample_vcf):
+		headline = re.match('^\#',line)
+		if headline is not None:
+			pass
+		else:
+			line = line.strip()
+			strings = line.split('\t')
+			variant_id = '_'.join([strings[0],strings[1]])
+			# check if the variants location is duplicated
+			if variant_id in var_dup:
+				outLine = '\t'.join(strings) + '\t' + '.' +'\t' + '.' + '\t' + 'dupVar' + '\n'
+				outfile.write(outLine)
+			else:
+				# pre-define
+				pcr_consensus = ''
+				pcr_free_consensus = ''
+				consensus_call = ''
+				# pcr 
+				pcr = itemgetter(*[9,10,11,12,14,15,16,23,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41])(strings)
+				SEQ2000 = decide_by_rep(pcr[0:4])
+				SEQ500 = decide_by_rep(pcr[4:7])
+				Nova = decide_by_rep(pcr[7:11])
+				XTen_ARD = decide_by_rep(pcr[11:14])
+				XTen_NVG = decide_by_rep(pcr[14:17])
+				XTen_WUX_1 = decide_by_rep(pcr[17:20])
+				XTen_WUX_2 = decide_by_rep(pcr[20:23])
+				sequence_site = [SEQ2000,SEQ500,Nova,XTen_ARD,XTen_NVG,XTen_WUX_1,XTen_WUX_2]
+				sequence_dict = Counter(sequence_site)
+				highest_sequence = sequence_dict.most_common(1)
+				candidate_sequence = highest_sequence[0][0]
+				freq_sequence = highest_sequence[0][1]
+				if freq_sequence > 4:
+					pcr_consensus = candidate_sequence
+				else:
+					pcr_consensus = 'inconSequenceSite'
+				# pcr-free
+				pcr_free = itemgetter(*[13,17,18,19,20,21,22,24,25,26])(strings)
+				SEQ2000 = decide_by_rep(pcr_free[0])
+				Nova_ARD_1 = decide_by_rep(pcr_free[1:4])
+				Nova_ARD_2 = decide_by_rep(pcr_free[4:7])
+				Nova_BRG = decide_by_rep(pcr_free[7:10])
+				sequence_site = [SEQ2000,Nova_ARD_1,Nova_ARD_2,Nova_BRG]
+				highest_sequence = sequence_dict.most_common(1)
+				candidate_sequence = highest_sequence[0][0]
+				freq_sequence = highest_sequence[0][1]
+				if freq_sequence > 2:
+					pcr_free_consensus = candidate_sequence
+				else:
+					pcr_free_consensus = 'inconSequenceSite'
+				# pcr and pcr-free
+				tag = ['inconGT','noInfo','inconMen','inconSequenceSite']
+				if (pcr_consensus == pcr_free_consensus) and (pcr_consensus not in tag) and (pcr_consensus != '0/0'):
+					consensus_call = pcr_consensus
+					strings[6] = 'reproducible'
+				elif (pcr_consensus in tag) or (pcr_free_consensus in tag):
+					consensus_call = 'filtered'
+					strings[6] = '.'
+				elif (pcr_consensus == '0/0') and (pcr_free_consensus not in tag) and (pcr_free_consensus != '0/0'):
+					consensus_call = 'pcr-free-speicifc'
+					strings[6] = '.'
+				elif (pcr_consensus != '0/0') and (pcr_consensus not in tag) and (pcr_free_consensus == '0/0'):
+					consensus_call = 'pcr-speicifc'
+					strings[6] = '.'
+				elif (pcr_consensus == '0/0') and (pcr_free_consensus == '0/0'):
+					consensus_call = 'confirm for parents'
+					strings[6] = '.'					
+				else:
+					consensus_call = 'filtered'
+					strings[6] = '.'
+				# percentage
+				percentage = vote_percentage(strings[9:])
+				strings[7] = 'PCT=' + percentage
+				# output 
+				outLine = '\t'.join(strings) + '\t' + pcr_consensus +'\t' + pcr_free_consensus + '\t' + consensus_call + '\n'
+				outfile.write(outLine)
+
+
+if __name__ == '__main__':
+	main()
+
+
+
+
+
+
+
+
+
+
+
+

codescripts/reformVCF.py

 
 # default columns, which will be included in the included in the calssifier
 vcfheader = '''##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="Voted by at least two replicates, six callers and two sequencing sites">
+##FILTER=<ID=PASS,Description="the same genotype between twin sister and mendelian consistent in 578 and 678">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=sister,Number=0,Type=Flag,Description="0 for sister consistent, 1 for sister inconsistent">
-##INFO=<ID=trioLCL5,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
-##INFO=<ID=trioLCL6,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
+##FORMAT=<ID=TWINS,Number=0,Type=Flag,Description="0 for sister consistent, 1 for sister inconsistent">
+##FORMAT=<ID=TRIO5,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
+##FORMAT=<ID=TRIO6,Number=0,Type=Flag,Description="0 for trio consistent, 1 for trio inconsistent">
 ##contig=<ID=chr1,length=248956422>
 ##contig=<ID=chr2,length=242193529>
 ##contig=<ID=chr3,length=198295559>
 		pass
 	# sister
 	if strings[11] == strings[14]:
-		info = "sister=1"
+		add_format = ":1"
 	else:
-		info = "sister=0"
+		add_format = ":0"
 	# trioLCL5
 	if strings[15] == 'MD=1':
-		info = info + ";trioLCL5=1"
+		add_format = add_format + ":1"
 	else:
-		info = info + ";trioLCL5=0"
+		add_format = add_format + ":0"
 	# trioLCL6
 	if strings[7] == 'MD=1':
-		info = info + ";trioLCL6=1"
+		add_format = add_format + ":1"
 	else:
-		info = info + ";trioLCL6=0"
+		add_format = add_format + ":0"
+	# filter
+	if (strings[11] == strings[14]) and (strings[15] == 'MD=1') and (strings[7] == 'MD=1'):
+		strings[6] = 'PASS'
+	else:
+		strings[6] = '.'
 	# output LCL5
-	LCL5outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+strings[5]+'\t'+strings[6]+'\t'+ info +'\t'+ strings[8] + '\t' + strings[14] + '\n'
+	LCL5outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+'.'+'\t'+strings[6]+'\t'+ '.' +'\t'+ 'GT:TWINS:TRIO5:TRIO6' + '\t' + strings[14] + add_format + '\n'
 	LCL5file.write(LCL5outLine)
 	# output LCL6
-	LCL6outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+strings[5]+'\t'+strings[6]+'\t'+ info +'\t'+ strings[8] + '\t' + strings[11] + '\n'
+	LCL6outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+'.'+'\t'+strings[6]+'\t'+ '.' +'\t'+ 'GT:TWINS:TRIO5:TRIO6' + '\t' + strings[11] + add_format + '\n'
 	LCL6file.write(LCL6outLine)
 	# output LCL7
-	LCL7outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+strings[5]+'\t'+strings[6]+'\t'+ info +'\t'+ strings[8] + '\t' + strings[10] + '\n'
+	LCL7outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+'.'+'\t'+strings[6]+'\t'+ '.' +'\t'+ 'GT:TWINS:TRIO5:TRIO6' + '\t' + strings[10] + add_format + '\n'
 	LCL7file.write(LCL7outLine)
 	# output LCL8
-	LCL8outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+strings[5]+'\t'+strings[6]+'\t'+ info +'\t'+ strings[8] + '\t' + strings[9] + '\n'
+	LCL8outLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+'.'+'\t'+strings[6]+'\t'+ '.' +'\t'+ 'GT:TWINS:TRIO5:TRIO6' + '\t' + strings[9] + add_format + '\n'
 	LCL8file.write(LCL8outLine)
 	# output family
-	familyoutLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+strings[5]+'\t'+strings[6]+'\t'+ info +'\t'+ strings[8] + '\t' + strings[14] + '\t' + strings[11] + '\t' + strings[10] + '\t' + strings[9] + '\n'
+	familyoutLine = strings[0]+'\t'+strings[1]+'\t'+strings[2]+'\t'+strings[3]+'\t'+strings[4]+'\t'+ '.'+'\t'+strings[6]+'\t'+ '.' +'\t'+ 'GT:TWINS:TRIO5:TRIO6' + '\t' + strings[14] + add_format +'\t' + strings[11] + add_format + '\t' + strings[10] + add_format +'\t' + strings[9] + add_format + '\n'
 	familyfile.write(familyoutLine)
 
 

inputs

   "{{ project_name }}.LCL7merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.LCL6familyzipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.LCL7votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.1",
+  "{{ project_name }}.LCL6votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.1",
   "{{ project_name }}.LCL5VCFrename.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL6mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.mergeSister.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL6merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL6variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
   "{{ project_name }}.LCL6zipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.LCL5votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.1",
   "{{ project_name }}.LCL7familyzipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL5familyzipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL6VCFrename.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.LCL5merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.LCL8votes.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.1",
   "{{ project_name }}.reformVCF.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.1",
   "{{ project_name }}.LCL5zipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }
 
+

tasks/indelNorm.wdl

+task indelNorm {
+	File vcf
+	File ref_dir
+	String fasta
+	String sampleName
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${vcf} | grep '#' > header
+		cat ${vcf} | grep -v '#' > body
+		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX\' > body.filtered
+		cat header body.filtered > ${sampleName}.filtered.vcf
+
+		/opt/hall-lab/bcftools-1.9/bin/bcftools norm -f ${ref_dir}/${fasta} ${sampleName}.filtered.vcf > ${sampleName}.normed.vcf
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File normed_vcf = "${sampleName}.normed.vcf"
+	}
+}

tasks/merge.wdl

 
 		rtg vcfmerge --force-merge-all --no-gzip -o ${sample}.merged.vcf ${sep=" " family_vcf_gz}
 
+		cat ${sample}.merged.vcf | grep -v '#' | cut -f1-2 | sed s'/\t/_/g' | sort | uniq -c | sed 's/\s\+/\t/g' | awk '{ if ($1 != 1) { print } }' | cut -f3 > ${sample}.vcf_dup.txt
+
 	>>>
 
 	runtime {
 	}
 	output {
 		File merged_vcf = "${sample}.merged.vcf"
+		File vcf_dup = "${sample}.vcf_dup.txt"
 	}
 }

tasks/votes.wdl

 task votes {
-	Array[File] mother_vcf_gz
-	Array[File] mother_vcf_idx
-	Array[File] father_vcf_gz
-	Array[File] father_vcf_idx
-	Array[File] twins_vcf_gz
-	Array[File] twins_vcf_idx
+	File merged_vcf
+	String vcf_dup
+	String sample
+	String prefix
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.sister.consistent.merged.vcf ${sep=" " mother_vcf_gz}
-
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.sister.consistent.merged.vcf ${sep=" " father_vcf_gz}
-
-		rtg vcfmerge --force-merge-all --no-gzip -o Twins.sister.consistent.vcf ${sep=" " twins_vcf_gz}
+		python /opt/high_confidence_call_vote.py -vcf ${merged_vcf} -dup ${vcf_dup} -sample ${sample} -prefix ${prefix}
 	>>>
 
 	runtime {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File mother_merged_vcf = "LCL8.sister.consistent.merged.vcf"
-		File father_merged_vcf = "LCL7.sister.consistent.merged.vcf"
-		File twins_merged_vcf = "Twins.sister.consistent.merged.vcf"
+		File annotated_vcf = "${prefix}_annotated.vcf"
 	}
 }

workflow.wdl

 import "./tasks/mergeSister.wdl" as mergeSister
 import "./tasks/reformVCF.wdl" as reformVCF
 import "./tasks/merge.wdl" as merge
+import "./tasks/votes.wdl" as votes
 
 workflow {{ project_name }} {
 	File inputSamplesFile
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+	call votes.votes as LCL5votes{
+		input:
+		merged_vcf=LCL5merge.merged_vcf,
+		vcf_dup=LCL5merge.vcf_dup,
+		sample='LCL5',
+		prefix='LCL5_consensus',
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 	call merge.merge as LCL6merge {
 		input:
 		family_vcf_gz=LCL6familyzipIndex.vcf_gz,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+	call votes.votes as LCL6votes {
+		input:
+		merged_vcf=LCL6merge.merged_vcf,
+		vcf_dup=LCL6merge.vcf_dup,
+		sample='LCL6',
+		prefix='LCL6_consensus',
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 	call merge.merge as LCL7merge {
 		input:
 		family_vcf_gz=LCL7familyzipIndex.vcf_gz,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+	call votes.votes as LCL7votes {
+		input:
+		merged_vcf=LCL7merge.merged_vcf,
+		vcf_dup=LCL7merge.vcf_dup,
+		sample='LCL7',
+		prefix='LCL7_consensus',
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 	call merge.merge as LCL8merge {
 		input:
 		family_vcf_gz=LCL8familyzipIndex.vcf_gz,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+	call votes.votes as LCL8votes {
+		input:
+		merged_vcf=LCL8merge.merged_vcf,
+		vcf_dup=LCL8merge.vcf_dup,
+		sample='LCL8',
+		prefix='LCL8_consensus',
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 }