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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
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Alternate genotype with no alternate allele in VCF output #116

Open tatumdmortimer opened 4 years ago

tatumdmortimer commented 4 years ago

I am using pilon v 1.16 to call variants from bacterial WGS data. I've noticed that occasionally in the VCF output the genotype will be called 1/1 but no alternate allele is listed. This seems to occur in regions where a deletion has been called.

Here as an example including the line before and after in the VCF: NC_011035.1 2149833 . A . 2289 Del DP=71;TD=72;BQ=32;MQ=60;QD=32;BC=71,0,0,0;QP=100,0,0,0;PC=112;IC=0;DC=0;XC=0;AC=0;AF=0.00 GT 0/0 NC_011035.1 2149834 . T . . Del DP=0;TD=73;BQ=0;MQ=60;QD=0;BC=0,0,0,0;QP=0,0,0,0;PC=113;IC=0;DC=71;XC=1;AC=2;AF=0.00 GT 1/1 NC_011035.1 2149835 . T . 2277 PASS DP=71;TD=73;BQ=33;MQ=60;QD=32;BC=1,0,0,70;QP=1,0,0,99;PC=113;IC=0;DC=0;XC=0;AC=0;AF=0.00 GT 0/0

Is there any significance to these calls? They cause an error when merging VCFs with bcftools.

ybendana commented 4 years ago

I'm using pilon 1.23 and I haven't seen this issue, I would try updating your version and see if it goes away. In my case I was getting confused by the 'Del' filter status. Somewhere before these lines you should see a record for the genotype 1/1 describing a deletion of several bases. Then the records following that will be for genotype 0/0 reporting reads that do not have the deletion. It became clear when I read the definition of Del:

FILTER=