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  • merge-vcf yielding '.' for ALT

    I converted some files to vcf with my own script and am trying to merge them using vcf-merge. Each file is its own sample. They appear to merge fine, but I am given '.' as the ALT instead of 'C,T' or whatever it should be.

    Lines from one of the input files:
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 27MS2
    chr1 67403777 rs6682922 C T . RD DB GT:VF:GN:FX .|.:H:IL23R:Promoter
    chr1 67403999 . T C . RD . GT:VF:GN:FX .|.:B:IL23R:Promoter

    Lines from the output file:
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 27MS2 27MS3 27MS4
    chr1 67403777 rs6682922 C . . RD AC=0;AN=0;DB;SF=0f,1f,2f GT:FX:VF:GN .|.:Promoter:47.0707:IL23R .|.:Promoter:60.2070:IL23R .|.:Promoter:38.0866:IL23R
    chr1 67403999 . T . . RD AC=0;AN=0;SF=0f GT:FX:VF:GN .|.:Promoter:8.2149:IL23R . .

    Why is it displaying '.' instead of the ALTs?
    Last edited by nikkiat; 04-20-2012, 09:03 AM.

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