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Output VCF file format #5

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Rhunos opened this issue Sep 21, 2015 · 0 comments
Open

Output VCF file format #5

Rhunos opened this issue Sep 21, 2015 · 0 comments

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@Rhunos
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Rhunos commented Sep 21, 2015

Correct me if I'm wrong, but I believe that there is a small inconsistency with the output VCF file and the VCFv4.1 specification (http://samtools.github.io/hts-specs/VCFv4.1.pdf) section 1.4.2 on Genotype fields.

At the moment a variant is notated as follows:

#CHROM  POS         ID              REF ALT QUAL    FILTER  INFO    FORMAT  1483JS0009
22      17072483    22:17072483:A:G A   G   .       PASS    X1:X2   CN:GT   C:0/1   

I believe the genotype data and its FORMAT should have the GT field at position 0, like:

#CHROM  POS         ID              REF ALT QUAL    FILTER  INFO    FORMAT  1483JS0009
22      17072483    22:17072483:A:G A   G   .       PASS    X1:X2   GT:CN   0/1:C   

I've been having some trouble with a few tools due to this. A small program on my side fixes the problem, but I figured you would like to know about this.

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