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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.
The text was updated successfully, but these errors were encountered:
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:
I believe the genotype data and its FORMAT should have the GT field at position 0, like:
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.
The text was updated successfully, but these errors were encountered: