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Filtering Vcf Files

I am trying to subset a VCF file by a tag in INFO column. The tag is a triplet and I want to threshold by one of the values in the triplet. For example, for a given record, my triplet would be ABC=1,2,3 and I would like to decide whether it should be in my set or not by ABC[1] > 23. How can I accomplish this?

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updated by Biostar Biostar • written by rickyflintoff • rickyflintoff

1 answer

you could use the following awk script:

/^#/    { print; next;}
/^[^#]/ {
    n=split($8,a,/;/);
    p=1;
    for(i=1;i<=n;++i)
        {
        m=split(a[i],b,/=/);
        if(m<2 || b[1]!="ABC") continue;
        split(b[2],c,/,/);
        if(int(c[2])>23) {p=0;}
        break;
        }
    if(p) print;
    }

usage:

awk -f filter.awk < input.vcf > output.vcf
• 80 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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