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Set Genotype Of Specific Sample/Genotype Comb To Unknown In Multisample Vcf File

I am running QC on a exomeseq dataset with a family structure. I would like to remove the Mendelian inconsistencies that I found: even with a high genotype quality threshold this occurs more often than expected. I ran into many programs to extract these Mendelian inconsistencies , but I like to set it to zero. (well actually ./.) . Does someone have same pointers to go from here?

To make it more clear the file of genotypes/sample id looks like this:

ID2   SNP34
ID3   SNP43
vcf qualitycontrol
• 3,664 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Maarten • Maarten

1 answer

I quickly wrote a tool for this: https://github.com/lindenb/jvarkit/wiki/Biostar86363

$ cat reset.txt
20    14370    NA00001
20    1234567    NA00003
20    1110696    NA00002

$ curl "https://raw.github.com/jamescasbon/PyVCF/master/vcf/test/example-4.1.vcf" |\
  java -jar dist/biostar86363.jar -G reset.txt 

##fileformat=VCFv4.1
##FILTER=<ID=q10,Description="Quality below="" 10"="">
##FILTER=<ID=s50,Description="Less than="" 50%="" of="" samples="" have="" data"="">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"="">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"="">
##FORMAT=<ID=GR,Number=1,Type=Integer,Description="(1) =="" Genotype="" was="" reset="" by="" Biostar86363="" "="">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"="">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"="">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"="">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership,="" build="" 129"="">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"="">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"="">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of="" Samples="" With="" Data"="">
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy="x">
##fileDate=20090805
##phasing=partial
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##source=myImputationProgramV3.1
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    NA00001    NA00002    NA00003
20    14370    rs6054257    G    A    29    PASS    AF=0.5;DB;DP=14;H2;NS=3    GT:DP:GQ:GR:HQ    .|.:1:48:1:51,51    1|0:8:48:0:51,51    1/1:5:43:0
20    17330    .    T    A    3    q10    AF=0.017;DP=11;NS=3    GT:GQ:DP:HQ    0|0:49:3:58,50    0|1:3:5:65,3    0/0:41:3
20    1110696    rs6040355    A    G,T    67    PASS    AA=T;AF=0.333,0.667;DB;DP=10;NS=2    GT:DP:GQ:GR:HQ    1|2:6:21:0:23,27    .|.:0:2:1:18,2    2/2:4:35:0
20    1230237    .    T    .    47    PASS    AA=T;DP=13;NS=3    GT:GQ:DP:HQ    0|0:54:7:56,60    0|0:48:4:51,51    0/0:61:2
20    1234567    microsat1    GTC    G,GTCT    50    PASS    AA=G;DP=9;NS=3    GT:DP:GQ:GR    0/1:4:35:0    0/2:2:17:0    ./.:3:40:1
• 147 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Awesome you made this. It is working indeed. The only thing I had to do is to change the access numbers to a position.(join to the rescue! )

• 0 views • link
written by Maarten • Maarten

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