g.vcf
shinlin77 opened this issue · 1 comments
shinlin77 commented
The output of my run was
chr1 2123373 . T <NON_REF> 0 . END=2123373 GT:GQ:MIN_DP:PL ./.:0:24:719,72,0
chr1 2123374 . G <NON_REF> 0 . END=2123374 GT:GQ:MIN_DP:PL ./.:0:26:101,0,521
chr1 2123375 . T <NON_REF> 0 . END=2123376 GT:GQ:MIN_DP:PL 0/0:48:26:0,48,719
GATK had a problem with the last line. I think the it should be END=2123375, right?
shinlin77 commented
GATK still doesn't like it but the END= isn't the issue.