first commit

README.md

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+#高置信位点整合Part2——从VCF和BAM文件中提取突变位点的信息
+
+> Author： Run Luyao
+>
+> E-mail：18110700050@fudan.edu.cn
+>
+> Git: http://choppy.3steps.cn/renluyao/HCC_Extract_Info.git
+>
+> Last Updates: 11/9/2019
+
+## 安装指南
+
+```bash
+# 激活choppy环境
+source activate choppy
+# 安装app
+choppy install renluyao/HCC_Extract_Info
+```
+
+## App概述
+
+当我们拿到测序结果的时候，没有办法判断哪些是真的突变位点，哪些是假阳性
+
+## 流程与参数
+
+两个问题：
+
+1. MNP
+2. merge之后的pos相同，但是ref和alt不同
+
+是不是gatk的问题，尝试用bcftools norm
+
+## App输入变量与输入文件
+
+## App输出文件
+
+## 结果展示与解读
+
+## CHANGELOG
+
+## FAQ
+

codescripts/bed_for_bamReadcount.py

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+import sys,getopt
+import os
+import re
+import fileinput
+
+def usage():
+    print(
+        """
+Usage: python bed_for_bamReadcount.py -i input_vcf_file -o prefix
+
+This script selects SNPs and Indels supported by all callsets.
+
+Please notice that bam-readcount only takes in 1-based coordinates.
+
+Input:
+-i a vcf file
+
+Output:
+-o  a indel bed file for bam-readcount
+        """)
+
+# select supported small variants
+def process(oneLine):
+    m = re.match('^\#',oneLine)
+    if m is not None:
+        pass
+    else:
+        line = oneLine.rstrip()
+        strings = line.strip().split('\t')
+        # convert the position to bed file for bam-readcount
+        # deletion
+        if len(strings[3]) > 1 and len(strings[4]) == 1:
+            pos = int(strings[1]) + 1
+            outline = strings[0] + '\t' + str(pos) + '\t' + str(pos) + '\t' + strings[3] + '\t' + strings[4]+'\n'
+            outINDEL.write(outline)
+        # insertion
+        elif len(strings[3]) == 1 and len(strings[4]) > 1 and (',' not in strings[4]):
+            outline = strings[0] + '\t' + strings[1] + '\t' + strings[1] +  '\t' + strings[3] +  '\t' + strings[4] + '\n'
+            outINDEL.write(outline)
+        else:
+            outMNP.write(oneLine)
+
+opts,args = getopt.getopt(sys.argv[1:],"hi:o:")
+for op,value in opts:
+    if op == "-i":
+        inputFile=value
+    elif op == "-o":
+        prefix=value    
+    elif op == "-h":
+        usage()
+        sys.exit()
+
+if len(sys.argv[1:]) < 3:
+    usage()
+    sys.exit()
+
+INDELname = prefix + '.bed'
+MNPname = prefix + '_MNP.txt'
+
+outINDEL = open(INDELname,'w')
+outMNP = open(MNPname,'w')
+
+for line in fileinput.input(inputFile):
+    process(line)
+
+outINDEL.close()
+outMNP.close()
+

codescripts/extract_vcf_information.py

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+import sys,getopt
+import os
+import re
+import fileinput
+import pandas as pd
+
+def usage():
+	print(
+		"""
+Usage: python extract_vcf_information.py -i input_merged_vcf_file -o parsed_file
+
+This script will extract SNVs and Indels information from the vcf files and output a tab-delimited files.
+
+Input:
+-i the selected vcf file
+
+Output:
+-o tab-delimited parsed file
+		""")
+
+# select supported small variants
+def process(oneLine):
+	line = oneLine.rstrip()
+	strings = line.strip().split('\t')
+	infoParsed = parse_INFO(strings[7])
+	formatKeys = strings[8].split(':')
+	formatValues = strings[9].split(':')
+	for i in range(0,len(formatKeys) -1) :
+		if formatKeys[i] == 'AD':
+			ra = formatValues[i].split(',')
+			infoParsed['RefDP'] = ra[0]
+			infoParsed['AltDP'] = ra[1]
+			if (int(ra[1]) + int(ra[0])) != 0:
+				infoParsed['af'] = float(int(ra[1])/(int(ra[1]) + int(ra[0])))
+			else:
+				pass
+		else:
+			infoParsed[formatKeys[i]] = formatValues[i]
+	infoParsed['chromo'] = strings[0]
+	infoParsed['pos'] = strings[1]
+	infoParsed['id'] = strings[2]
+	infoParsed['ref'] = strings[3]
+	infoParsed['alt'] = strings[4]
+	infoParsed['qual'] = strings[5]
+	return infoParsed
+
+
+def parse_INFO(info):
+	strings = info.strip().split(';')
+	keys = []
+	values = []
+	for i in strings:
+		kv = i.split('=')
+		if kv[0] == 'DB':
+			keys.append('DB')
+			values.append('1')
+		elif kv[0] == 'AF':
+			pass
+		elif kv[0] == 'POSITIVE_TRAIN_SITE':
+			pass
+		elif kv[0] == 'NEGATIVE_TRAIN_SITE':
+			pass
+		else:
+			keys.append(kv[0])
+			values.append(kv[1])
+	infoDict = dict(zip(keys, values))
+	return infoDict
+	
+
+opts,args = getopt.getopt(sys.argv[1:],"hi:o:") 
+for op,value in opts:
+	if op == "-i":
+		inputFile=value
+	elif op == "-o":
+		outputFile=value	
+	elif op == "-h":
+		usage()
+		sys.exit()
+
+if len(sys.argv[1:]) < 3:
+	usage()
+	sys.exit()
+
+allDict = []
+for line in fileinput.input(inputFile):
+	m = re.match('^\#',line)
+	if m is not None:
+		pass
+	else:
+		oneDict = process(line)
+		allDict.append(oneDict)
+
+allTable = pd.DataFrame(allDict)
+
+allTable.to_csv(outputFile,sep='\t',index=False)
+

codescripts/oneClass.py

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+# import modules
+import numpy as np
+import pandas as pd
+from sklearn import svm
+from sklearn import preprocessing
+import sys, argparse, os
+from vcf2bed import position_to_bed,padding_region
+
+
+
+parser = argparse.ArgumentParser(description="this script is to preform one calss svm on each chromosome")
+
+parser.add_argument('-train', '--trainDataset', type=str, help='training dataset generated from extracting vcf information part, with mutaitons supported by callsets',  required=True)
+parser.add_argument('-test', '--testDataset', type=str, help='testing dataset generated from extracting vcf information part, with mutaitons not called by all callsets',  required=True)
+parser.add_argument('-name', '--sampleName', type=str, help='sample name for output file name',  required=True)
+
+args = parser.parse_args()
+
+# Rename input:
+train_input = args.trainDataset
+test_input = args.testDataset
+sample_name = args.sampleName
+
+# default columns, which will be included in the included in the calssifier
+chromosome = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15' ,'chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX','chrY']
+feature_heter_cols = ['AltDP','BaseQRankSum','DB','DP','FS','GQ','MQ','MQRankSum','QD','ReadPosRankSum','RefDP','SOR','af']
+feature_homo_cols = ['AltDP','DB','DP','FS','GQ','MQ','QD','RefDP','SOR','af']
+
+
+# import datasets sepearate the records with or without BaseQRankSum annotation, etc.
+def load_dat(dat_file_name):
+    dat = pd.read_table(dat_file_name)
+    dat['DB'] = dat['DB'].fillna(0)
+    dat = dat[dat['DP'] != 0]
+    dat['af'] = dat['AltDP']/(dat['AltDP'] + dat['RefDP'])
+    homo_rows = dat[dat['BaseQRankSum'].isnull()]
+    heter_rows = dat[dat['BaseQRankSum'].notnull()]
+    return homo_rows,heter_rows
+
+
+train_homo,train_heter = load_dat(train_input)
+test_homo,test_heter = load_dat(test_input)
+clf = svm.OneClassSVM(nu=0.05,kernel='rbf', gamma='auto_deprecated',cache_size=500)
+
+def prepare_dat(train_dat,test_dat,feature_cols,chromo):
+	chr_train = train_dat[train_dat['chromo'] == chromo]
+	chr_test = test_dat[test_dat['chromo'] == chromo]
+	
+	train_dat = chr_train.loc[:,feature_cols]
+	test_dat = chr_test.loc[:,feature_cols]
+	train_dat_scaled = preprocessing.scale(train_dat)
+	test_dat_scaled = preprocessing.scale(test_dat)
+	return chr_test,train_dat_scaled,test_dat_scaled
+
+def oneclass(X_train,X_test,chr_test):
+	clf.fit(X_train)
+	y_pred_test = clf.predict(X_test)
+	test_true_dat = chr_test[y_pred_test == 1]
+	test_false_dat = chr_test[y_pred_test == -1]
+	return test_true_dat,test_false_dat
+
+predicted_true = pd.DataFrame(columns=train_homo.columns)
+predicted_false = pd.DataFrame(columns=train_homo.columns)
+
+for chromo in chromosome:
+	# homo datasets
+	chr_test_homo,X_train_homo,X_test_homo = prepare_dat(train_homo,test_homo,feature_homo_cols,chromo)
+	test_true_homo,test_false_homo = oneclass(X_train_homo,X_test_homo,chr_test_homo)
+	predicted_true = predicted_true.append(test_true_homo)
+	predicted_false = predicted_false.append(test_false_homo)
+	# heter datasets
+	chr_test_heter,X_train_heter,X_test_heter = prepare_dat(train_heter,test_heter,feature_heter_cols,chromo)
+	test_true_heter,test_false_heter = oneclass(X_train_heter,X_test_heter,chr_test_heter)
+	predicted_true = predicted_true.append(test_true_heter)
+	predicted_false = predicted_false.append(test_false_heter)
+
+predicted_true_filename = sample_name + '_predicted_true.txt'
+predicted_false_filename = sample_name + '_predicted_false.txt'
+
+predicted_true.to_csv(predicted_true_filename,sep='\t',index=False)
+predicted_false.to_csv(predicted_false_filename,sep='\t',index=False)
+
+# output the bed file and padding bed region 50bp
+
+predicted_true_bed_filename = sample_name + '_predicted_true.bed'
+predicted_false_bed_filename = sample_name + '_predicted_false.bed'
+padding_filename = sample_name + '_padding.bed'
+
+predicted_true_bed = open(predicted_true_bed_filename,'w')
+predicted_false_bed = open(predicted_false_bed_filename,'w')
+padding = open(padding_filename,'w')
+
+#
+for index,row in predicted_false.iterrows():
+	chromo,pos1,pos2 = position_to_bed(row['chromo'],row['pos'],row['ref'],row['alt'])
+	outline_pos = chromo + '\t' + str(pos1) + '\t' + str(pos2) + '\n'
+	predicted_false_bed.write(outline_pos)
+	chromo,pad_pos1,pad_pos2,pad_pos3,pad_pos4 = padding_region(chromo,pos1,pos2,50)
+	outline_pad_1 = chromo + '\t' + str(pad_pos1) + '\t' + str(pad_pos2) + '\n'
+	outline_pad_2 = chromo + '\t' + str(pad_pos3) + '\t' + str(pad_pos4) + '\n'
+	padding.write(outline_pad_1)
+	padding.write(outline_pad_2)
+
+for index,row in predicted_true.iterrows():
+	chromo,pos1,pos2 = position_to_bed(row['chromo'],row['pos'],row['ref'],row['alt'])
+	outline_pos = chromo + '\t' + str(pos1) + '\t' + str(pos2) + '\n'
+	predicted_true_bed.write(outline_pos)
+
+

codescripts/select_small_variants_supported_by_all_callsets.py

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+import sys,getopt
+import os
+import re
+import fileinput
+
+def usage():
+	print(
+		"""
+Usage: python select_small_variants_supported_by_all_callsets.py -i input_merged_vcf_file -o prefix
+
+This script selects SNPs and Indels supported by all callsets.
+
+Input:
+-i a merged vcf file
+
+Output:
+-o  a vcf file containd the selected SNPs and Indels
+		""")
+
+# select supported small variants
+def process(oneLine):
+	m = re.match('^\#',oneLine)
+	if m is not None:
+		outVCF.write(oneLine)
+		OUTname.write(oneLine)
+	else:
+		line = oneLine.rstrip()
+		strings = line.strip().split('\t')
+		gt = [i.split(':', 1)[0] for i in strings[9:len(strings)]]
+		if all(e == gt[0] for e in gt) and (gt[0] != '.'):
+			# output the record to vcf
+			outVCF.write(oneLine)
+		else:
+			OUTname.write(oneLine)
+
+
+opts,args = getopt.getopt(sys.argv[1:],"hi:o:")
+for op,value in opts:
+	if op == "-i":
+		inputFile=value
+	elif op == "-o":
+		prefix=value	
+	elif op == "-h":
+		usage()
+		sys.exit()
+
+if len(sys.argv[1:]) < 3:
+	usage()
+	sys.exit()
+
+VCFname = prefix + '.vcf'
+OUTname = prefix + '_outlier.vcf'
+
+outVCF = open(VCFname,'w')
+OUTname = open(OUTname,'w')
+
+for line in fileinput.input(inputFile):
+	process(line)
+
+outVCF.close()
+OUTname.close()
+

codescripts/vcf2bed.py

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+import re
+
+def position_to_bed(chromo,pos,ref,alt):
+    # snv
+    # Start cooridinate BED = start coordinate VCF - 1
+    # End cooridinate BED = start coordinate VCF 
+
+    if len(ref) == 1 and len(alt) == 1:
+        StartPos = int(pos) -1
+        EndPos = int(pos)
+    
+    # deletions
+    # Start cooridinate BED = start coordinate VCF - 1
+    # End cooridinate BED = start coordinate VCF + (reference length - alternate length)
+
+    elif len(ref) > 1 and len(alt) == 1:
+        StartPos = int(pos) - 1
+        EndPos = int(pos) + (len(ref) - 1)
+        
+    #insertions
+    # For insertions:
+    # Start cooridinate BED = start coordinate VCF - 1
+    # End cooridinate BED = start coordinate VCF + (alternate length - reference length)
+
+    else:
+        StartPos = int(pos) - 1
+        EndPos = int(pos) + (len(alt) - 1)
+
+    return chromo,StartPos,EndPos
+
+def padding_region(chromo,pos1,pos2,padding):
+    StartPos1 = pos1 - padding
+    EndPos1 = pos1
+    StartPos2 = pos2
+    EndPos2 = pos2 + padding
+    return chromo,StartPos1,EndPos1,StartPos2,EndPos2

family.tsv

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+Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_hc.vcf
+Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_hc.vcf
+Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_hc.vcf
+Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402_hc.vcf
+Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402_hc.vcf
+Quartet_DNA_BGI_SEQ500_BGI_LCL5_1_20180328	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_1_20180328_hc.vcf
+Quartet_DNA_BGI_SEQ500_BGI_LCL5_2_20180328	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_2_20180328_hc.vcf
+Quartet_DNA_BGI_SEQ500_BGI_LCL5_3_20180328	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_3_20180328_hc.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108_RAW.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108_RAW.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108_RAW.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111_RAW.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111_RAW.vcf
+Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111_RAW.vcf
+Quartet_DNA_ILM_Nova_BRG_LCL5_1_20171024	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_1_20171024_RAW.vcf
+Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930_RAW.vcf
+Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930_RAW.vcf
+Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930_RAW.vcf
+Quartet_DNA_ILM_Nova_GAC_LCL5_1_20171025	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_GAC_LCL5_1_20171025_RAW.vcf
+Quartet_DNA_ILM_Nova_NVG_LCL5_1_20171024	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_NVG_LCL5_1_20171024_RAW.vcf
+Quartet_DNA_ILM_Nova_WUX_LCL5_1_20171024	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_WUX_LCL5_1_20171024_RAW.vcf
+Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403_hc.vcf
+Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403_hc.vcf
+Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403_hc.vcf
+Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329_RAW.vcf
+Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329_RAW.vcf
+Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703_RAW.vcf
+Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703	oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703_RAW.vcf

inputs

@@ -0,0 +1,9 @@
+{
+  "{{ project_name }}.mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.sdf": "oss://chinese-quartet/quartet-storage-data/reference_data/GRCh38.d1.vd1.sdf/",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.KeepVar.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.0"
+}

tasks/ExtractVCFinfo.wdl

@@ -0,0 +1,34 @@
+task ExtractVCFinfo {
+	File snv_train
+	File snv_test
+	File indel_train
+	File indel_test
+	String snv_train_sampleName = basename(snv_train,".vcf")
+	String snv_test_sampleName = basename(snv_test,".vcf")
+	String indel_train_sampleName = basename(indel_train,".vcf")
+	String indel_test_sampleName = basename(indel_test,".vcf")	
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		python /opt/extract_vcf_information.py -i ${snv_train} -o ${snv_train_sampleName}.txt
+		python /opt/extract_vcf_information.py -i ${snv_test} -o ${snv_test_sampleName}.txt
+		python /opt/extract_vcf_information.py -i ${indel_train} -o ${indel_train_sampleName}.txt
+		python /opt/extract_vcf_information.py -i ${indel_test} -o ${indel_test_sampleName}.txt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File snv_train_vcf = "${snv_train_sampleName}.txt"
+		File snv_test_vcf = "${snv_test_sampleName}.txt"
+		File indel_train_vcf = "${indel_train_sampleName}.txt"
+		File indel_test_vcf = "${indel_test_sampleName}.txt"
+	}
+}

tasks/KeepVar.wdl

@@ -0,0 +1,26 @@
+task KeepVar {
+	File violation_merged_vcf
+	File consistent_merged_vcf
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		python /opt/select_small_variants_supported_by_all_callsets.py -i ${violation_merged_vcf} -o violation.all.selected
+
+		python /opt/select_small_variants_supported_by_all_callsets.py -i ${consistent_merged_vcf} -o consistent.all.selected
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File violation_keeped_vcf = "violation.all.selected.vcf"
+		File violation_outlier_vcf = "violation.all.selected_outlier.vcf"
+		File consistent_keeped_vcf = "consistent.all.selected.vcf"
+		File consistent_outlier_vcf = "consistent.all.selected_outlier.vcf"
+	}
+}

tasks/SepSnvIndel.wdl

@@ -0,0 +1,69 @@
+task SepSnvIndel {
+	File vcf
+	String sampleName = basename(vcf,".normed.vcf")
+	File keeped_vcf
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${vcf} | grep '#' > header
+		cat ${vcf} | sed '/^#/d' | awk '$5!~/,/' > removed.body
+		cat ${vcf} | sed '/^#/d' | awk '$5~/,/' > MNP.body
+		cat header removed.body > ${sampleName}.MNPremoved.vcf
+		cat header MNP.body > ${sampleName}.MNP.vcf
+
+		rtg bgzip ${sampleName}.MNPremoved.vcf
+		rtg index -f vcf ${sampleName}.MNPremoved.vcf.gz
+
+
+		rtg bgzip ${keeped_vcf} -c > all.selected.vcf.gz
+		rtg index -f vcf all.selected.vcf.gz
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.snv.train.vcf.gz --include-vcf=all.selected.vcf.gz --snps-only 
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.snv.test.vcf.gz --exclude-vcf=all.selected.vcf.gz --snps-only 
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.indel.train.vcf.gz --include-vcf=all.selected.vcf.gz --non-snps-only
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.indel.test.vcf.gz --exclude-vcf=all.selected.vcf.gz --non-snps-only
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.snv.vcf.gz --snps-only 
+
+		rtg vcffilter -i ${sampleName}.MNPremoved.vcf.gz -o ${sampleName}.normed.indel.vcf.gz --non-snps-only
+	
+
+		gzip -d ${sampleName}.normed.snv.train.vcf.gz -c > ${sampleName}.normed.snv.train.vcf
+		gzip -d ${sampleName}.normed.snv.test.vcf.gz -c > ${sampleName}.normed.snv.test.vcf
+		gzip -d ${sampleName}.normed.indel.train.vcf.gz -c > ${sampleName}.normed.indel.train.vcf
+		gzip -d ${sampleName}.normed.indel.test.vcf.gz -c > ${sampleName}.normed.indel.test.vcf
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File MNP="${sampleName}.MNP.vcf"
+		File snv_gz = "${sampleName}.normed.snv.vcf.gz"
+		File snv_idx = "${sampleName}.normed.snv.vcf.gz.tbi"
+		File indel_gz = "${sampleName}.normed.indel.vcf.gz"
+		File indel_idx = "${sampleName}.normed.indel.vcf.gz.tbi"
+		File snv_train = "${sampleName}.normed.snv.train.vcf"
+		File snv_test = "${sampleName}.normed.snv.test.vcf"
+		File indel_train = "${sampleName}.normed.indel.train.vcf"
+		File indel_test = "${sampleName}.normed.indel.test.vcf"
+		File snv_train_gz = "${sampleName}.normed.snv.train.vcf.gz"
+		File snv_test_gz = "${sampleName}.normed.snv.test.vcf.gz"
+		File indel_train_gz = "${sampleName}.normed.indel.train.vcf.gz"
+		File indel_test_gz = "${sampleName}.normed.indel.test.vcf.gz"
+		File snv_train_idx = "${sampleName}.normed.snv.train.vcf.gz.tbi"
+		File snv_test_idx = "${sampleName}.normed.snv.test.vcf.gz.tbi"
+		File indel_train_idx = "${sampleName}.normed.indel.train.vcf.gz.tbi"
+		File indel_test_idx = "${sampleName}.normed.indel.test.vcf.gz.tbi"		
+	}
+}

tasks/SepTrueFalse.wdl

@@ -0,0 +1,71 @@
+task SepTrueFalse {
+	File snv_true_bed
+	File snv_false_bed
+	File indel_true_bed
+	File indel_false_bed
+	File snv_padding
+	File indel_padding
+
+	File snv_gz
+	File indel_gz
+	File snv_idx
+	File indel_idx
+	File snv_test_gz
+	File indel_test_gz
+	File snv_test_idx
+	File indel_test_idx	
+
+	String sampleName = basename(snv_gz,".normed.snv.vcf.gz")
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+
+	rtg vcffilter -i ${snv_test_gz} -o ${sampleName}.true.snv.vcf.gz --include-bed=${snv_true_bed}
+
+	rtg vcffilter -i ${snv_test_gz} -o ${sampleName}.false.snv.vcf.gz --include-bed=${snv_false_bed}
+
+	rtg vcffilter -i ${snv_gz} -o ${sampleName}.remain.snv.vcf.gz --exclude-bed=${snv_false_bed}
+
+	rtg vcffilter -i ${snv_gz} -o ${sampleName}.padding.snv.vcf.gz --include-bed=${snv_padding}
+
+	
+	rtg vcffilter -i ${indel_test_gz} -o ${sampleName}.true.indel.vcf.gz --include-bed=${indel_true_bed}
+
+	rtg vcffilter -i ${indel_test_gz} -o ${sampleName}.false.indel.vcf.gz --include-bed=${indel_false_bed}
+
+	rtg vcffilter -i ${indel_gz} -o ${sampleName}.remain.indel.vcf.gz --exclude-bed=${indel_false_bed}
+
+	rtg vcffilter -i ${indel_gz} -o ${sampleName}.padding.indel.vcf.gz --include-bed=${indel_padding}
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File snv_true_vcf = "${sampleName}.true.snv.vcf.gz"
+		File snv_true_vcf_index = "${sampleName}.true.snv.vcf.gz.tbi"
+		File snv_false_vcf = "${sampleName}.false.snv.vcf.gz"
+		File snv_false_vcf_index = "${sampleName}.false.snv.vcf.gz.tbi"
+		File snv_remain_vcf = "${sampleName}.remain.snv.vcf.gz"
+		File snv_remain_vcf_index = "${sampleName}.remain.snv.vcf.gz.tbi"
+		File snv_padding_vcf = "${sampleName}.padding.snv.vcf.gz"
+		File snv_padding_vcf_index = "${sampleName}.padding.snv.vcf.gz.tbi"
+
+		File indel_true_vcf = "${sampleName}.true.indel.vcf.gz"
+		File indel_true_vcf_index = "${sampleName}.true.indel.vcf.gz.tbi"
+		File indel_false_vcf = "${sampleName}.false.indel.vcf.gz"
+		File indel_false_vcf_index = "${sampleName}.false.indel.vcf.gz.tbi"
+		File indel_remain_vcf = "${sampleName}.remain.indel.vcf.gz"
+		File indel_remain_vcf_index = "${sampleName}.remain.indel.vcf.gz.tbi"
+		File indel_padding_vcf = "${sampleName}.padding.indel.vcf.gz"
+		File indel_padding_vcf_index = "${sampleName}.padding.indel.vcf.gz.tbi"
+	}
+}
+

tasks/indelNorm.wdl

@@ -0,0 +1,29 @@
+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\|^chrY\|^chrM' > 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/mendelian.wdl

@@ -0,0 +1,58 @@
+task mendelian {
+	File mother_vcf_gz
+	File father_vcf_gz
+	File child_vcf_gz
+	File mother_vcf_idx
+	File father_vcf_idx
+	File child_vcf_idx
+	String mother_name
+	String father_name
+	String child_name
+	String family_name
+	File sdf
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		rtg vcfmerge -o family.vcf.gz ${mother_vcf_gz} ${father_vcf_gz} ${child_vcf_gz} 
+
+		rtg vcfannotate -i family.vcf.gz -o family.anno.vcf.gz \
+		--add-header "##SAMPLE=<ID=${mother_name},Sex=FEMALE>" \
+		--add-header "##SAMPLE=<ID=${father_name},Sex=MALE>" \
+		--add-header "##SAMPLE=<ID=${child_name},Sex=FEMALE>" \
+		--add-header "##PEDIGREE=<Child=${child_name},Mother=${mother_name},Father=${father_name}>"
+
+		rtg mendelian -i family.anno.vcf.gz -t ${sdf} -o ${family_name}.family.anno.mendelian.vcf.gz --lenient
+
+		zcat ${family_name}.family.anno.mendelian.vcf.gz | grep '#' > header
+		zcat ${family_name}.family.anno.mendelian.vcf.gz | grep -v '#'| grep 'MCU\|MCV' | cat header -  > ${family_name}.violation.vcf
+		zcat ${family_name}.family.anno.mendelian.vcf.gz | grep -v '#'| grep -v 'MCV' | grep -v 'MCU' > ${family_name}.consistent.vcf
+
+		rtg bgzip ${family_name}.violation.vcf 
+		rtg index -f vcf ${family_name}.violation.vcf.gz
+
+		rtg bgzip ${family_name}.consistent.vcf
+		rtg index -f vcf ${family_name}.consistent.vcf.gz
+
+		rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.violation.vcf.gz --include-vcf=${family_name}.violation.vcf.gz
+
+		rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.consistent.vcf.gz --include-vcf=${family_name}.consistent.vcf.gz		
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File family_vcf_gz = "${family_name}.family.anno.mendelian.vcf.gz"
+		File family_vcf_index = "${family_name}.family.anno.mendelian.vcf.gz.tbi"
+		File violation_vcf_gz = "${child_name}.violation.vcf.gz"
+		File violation_vcf_idx = "${child_name}.violation.vcf.gz.tbi"
+		File consistent_vcf_gz = "${child_name}.consistent.vcf.gz"
+		File consistent_vcf_idx = "${child_name}.consistent.vcf.gz.tbi"
+	}
+}

tasks/merge.wdl

@@ -0,0 +1,26 @@
+task merge {
+	Array[File] violation_vcf_gz
+	Array[File] violation_vcf_idx
+	Array[File] consistent_vcf_gz
+	Array[File] consistent_vcf_idx
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		rtg vcfmerge --force-merge-all --no-gzip -o all.violation.vcf ${sep=" " violation_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o all.consistent.vcf ${sep=" " consistent_vcf_gz}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File violation_merged_vcf = "all.violation.vcf"
+		File consistent_merged_vcf = "all.consistent.vcf"
+	}
+}
+

tasks/mergeBed.wdl

@@ -0,0 +1,35 @@
+task mergeBed {
+	Array[File] snv_true_bed
+	Array[File] snv_false_bed
+	Array[File] indel_true_bed
+	Array[File] indel_false_bed
+	Array[File]	indel_padding
+	Array[File] snv_padding
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_true_bed} ${sep=" " indel_true_bed}  > merged.true.bed
+
+	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_false_bed} ${sep=" " indel_false_bed}  > merged.false.bed
+
+	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_padding} ${sep=" " indel_padding}  > merged.padding.bed	
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File true_bed = "merged.true.bed"
+		File false_bed = "merged.false.bed"
+		File padding = "merged.padding.bed"
+	}
+}
+

tasks/mergeVCF.wdl

@@ -0,0 +1,61 @@
+task mergeVCF {
+	Array[File] snv_true_vcf
+	Array[File] snv_true_vcf_index
+	Array[File] snv_false_vcf
+	Array[File] snv_false_vcf_index
+	Array[File] snv_remain_vcf
+	Array[File] snv_remain_vcf_index
+	Array[File] snv_padding_vcf
+	Array[File] snv_padding_vcf_index
+
+	Array[File] indel_true_vcf
+	Array[File] indel_true_vcf_index
+	Array[File] indel_false_vcf
+	Array[File] indel_false_vcf_index
+	Array[File] indel_remain_vcf
+	Array[File] indel_remain_vcf_index 
+	Array[File] indel_padding_vcf
+	Array[File] indel_padding_vcf_index
+
+	String quartet_sample
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.snv.true.vcf.gz ${sep=" " snv_true_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.snv.false.vcf.gz ${sep=" " snv_false_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.snv.remain.vcf.gz ${sep=" " snv_remain_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.snv.padding.vcf.gz ${sep=" " snv_padding_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.indel.true.vcf.gz ${sep=" " indel_true_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.indel.false.vcf.gz ${sep=" " indel_false_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.indel.remain.vcf.gz ${sep=" " indel_remain_vcf}
+
+		rtg vcfmerge --force-merge-all --no-gzip -o ${quartet_sample}.indel.padding.vcf.gz ${sep=" " indel_padding_vcf}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File merged_snv_true = "${quartet_sample}.snv.true.vcf.gz"
+		File merged_snv_false = "${quartet_sample}.snv.false.vcf.gz"
+		File merged_snv_remain = "${quartet_sample}.snv.remain.vcf.gz"
+		File merged_snv_padding = "${quartet_sample}.snv.padding.vcf.gz"
+		File merged_indel_true = "${quartet_sample}.indel.true.vcf.gz"
+		File merged_indel_false = "${quartet_sample}.indel.false.vcf.gz"
+		File merged_indel_remain = "${quartet_sample}.indel.remain.vcf.gz"
+		File merged_indel_padding = "${quartet_sample}.indel.padding.vcf.gz"
+	}
+
+}

tasks/oneClass.wdl

@@ -0,0 +1,39 @@
+task oneClass {
+	File snv_train_vcf
+	File snv_test_vcf
+	File indel_train_vcf
+	File indel_test_vcf
+	String sampleName = basename(snv_train_vcf,".normed.snv.train.txt")
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+	python /opt/oneClass.py -train ${snv_train_vcf} -test ${snv_test_vcf} -name ${sampleName}_snv
+
+	python /opt/oneClass.py -train ${indel_train_vcf} -test ${indel_test_vcf} -name ${sampleName}_indel	
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File snv_true_txt = "${sampleName}_snv_predicted_true.txt"
+		File snv_false_txt = "${sampleName}_snv_predicted_false.txt"
+		File snv_true_bed = "${sampleName}_snv_predicted_true.bed"
+		File snv_false_bed = "${sampleName}_snv_predicted_false.bed"
+		File snv_padding = "${sampleName}_snv_padding.bed"
+		File indel_true_txt = "${sampleName}_indel_predicted_true.txt"
+		File indel_false_txt = "${sampleName}_indel_predicted_false.txt"
+		File indel_true_bed = "${sampleName}_indel_predicted_true.bed"
+		File indel_false_bed = "${sampleName}_indel_predicted_false.bed"
+		File indel_padding = "${sampleName}_indel_padding.bed"
+	}
+}
+

tasks/zipIndex.wdl

@@ -0,0 +1,37 @@
+task zipIndex {
+	File violation_vcf
+	File consistent_vcf
+	File child_vcf_gz
+	File child_vcf_idx
+	File child_name
+	String family_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		rtg bgzip ${violation_vcf} -c > ${family_name}.violation.vcf.gz
+		rtg index -f vcf ${family_name}.violation.vcf.gz
+
+		rtg bgzip ${consistent_vcf} -c > ${family_name}.consistent.vcf
+		rtg index -f vcf ${family_name}.consistent.vcf.gz
+
+		rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.violation.vcf.gz --include-vcf=${family_name}.violation.vcf.gz
+
+		rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.consistent.vcf.gz --include-vcf=${family_name}.consistent.vcf.gz		
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File violation_vcf_gz = "${child_name}.violation.vcf.gz"
+		File violation_vcf_idx = "${child_name}.violation.vcf.gz.tbi"
+		File consistent_vcf_gz = "${child_name}.consistent.vcf"
+		File consistent_vcf_idx = "${child_name}.consistent.vcf.tbi"
+	}
+}

workflow.wdl

@@ -0,0 +1,49 @@
+import "./tasks/mendelian.wdl" as mendelian
+import "./tasks/merge.wdl" as merge
+import "./tasks/KeepVar.wdl" as KeepVar
+ 
+workflow {{ project_name }} {
+	File inputSamplesFile
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	File sdf
+	String cluster_config
+	String disk_size
+
+	scatter (sample in inputSamples){
+		call mendelian.mendelian as mendelian {
+			input: 
+			mother_vcf_gz=sample[0],
+			father_vcf_gz=sample[1],
+			child_vcf_gz=sample[2],
+			mother_vcf_idx=sample[3],
+			father_vcf_idx=sample[4],
+			child_vcf_idx=sample[5],
+			mother_name=sample[6],
+			father_name=sample[7],
+			child_name=sample[8],
+			family_name=sample[9],
+			sdf=sdf,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
+	}
+
+	call merge.merge as merge {
+		input:
+		violation_vcf_gz=mendelian.violation_vcf_gz,
+		violation_vcf_idx=mendelian.violation_vcf_idx,
+		consistent_vcf_gz=mendelian.consistent_vcf_gz,
+		consistent_vcf_idx=mendelian.consistent_vcf_idx,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+	call KeepVar.KeepVar as KeepVar {
+		input:
+		violation_merged_vcf=merge.violation_merged_vcf,
+		consistent_merged_vcf=merge.consistent_merged_vcf,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+}