An integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing

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Input file introduction:

VCF file (version 4)

1: The format of VCF file name

• FamilyID.vcf.tar or *.tar.gz or *.gz or *.tar.bz2;
• FamilyID should be identical with family list file;
• Example: trios1.vcf.tar or *.tar.gz or *.gz or *.tar.bz2;

2: VCF (version 4) format

• VCF stands for variant call format. It is a text format consisting of a header section, which is optional, and an sequence variations section.
• A minimal VCF file might look like this:
• ##fileformat=VCFv4.1 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AX7 AX7S AX7F AX7M chr1 10091 . T G 51.12 TruthSensitivityTranche99.00to99.90 AB=0.692;AC=1;AF=0.17;AN=6;BaseQRankSum=-0.778;DP=33;Dels=0.00;FS=10.000;HRun=0;HaplotypeScore=2.1374;MQ=15.55;MQ0=19;MQRankSum=1.202;QD=3.93;ReadPosRankSum=-1.485;VQSLOD=-3.6787;culprit=QD GT:AD:DP:GQ:PL 0/0:11,0:11:3.01:0,3,42 0/1:11,3:11:5.43:0,3,35 0/1:9,4:13:55.38:85,0,55 0/0:7,2:9:5.99:0,6,55 chr1 724225 rs61769357 C T 54.91 PASS AB=0.379;AC=4;AF=0.67;AN=6;BaseQRankSum=0.000;DB;DP=14;Dels=0.00;FS=3.979;HRun=0;HaplotypeScore=10.1771;MQ=29.06;MQ0=5;MQRankSum=-0.720;QD=3.92;ReadPosRankSum=-0.720;VQSLOD=-2.1655;culprit=QD GT:AD:DP:GQ:PL 0/1:1,3:5:27.42:27,0,27 0/1:4,6:5:27.42:27,4,0 1/1:1,4:5:3.01:37,3,0 0/1:1,1:4:29.23:29,0,33 chr1 724229 . A G 155.19 PASS AB=0.250;AC=4;AF=0.67;AN=6;BaseQRankSum=0.067;DP=14;Dels=0.00;FS=6.021;HRun=0;HaplotypeScore=8.8444;MQ=29.06;MQ0=5;MQRankSum=-0.067;QD=11.09;ReadPosRankSum=0.067;VQSLOD=-2.6844;culprit=HaplotypeScore GT:AD:DP:GQ:PL 0/1:1,3:5:24.41:58,0,24 0/1:1,5:5:35.41:58,2,0 1/1:1,4:5:3.01:37,3,0 0/1:1,3:4:26.54:99,0,27

family list

1: The format of family list file name

No restriction for family list file name, It can be defined as family.list or disease.list or anything else.

2: family list format

family list file is a TAB-delimited text format containing four columns, each three rows contain the information of a family:

• 1) family ID
• 2) individual ID
• 3) relationship ( proband, sibling, father or mother )
• 4) proband sex (only in the row containing proband or sibling information, default "M")

A minimal family list file might look like this:

• trios1 AX7 Proband M trios1 AX7S Sibling M trios1 AX7F Father trios1 AX7M Mother trios2 AX17 Proband M trios2 AX17F Father trios2 AX17M Mother

Only a row containing proband information has four columns, "M" for male, while "F" for famale.

Copyright©2014, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.