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kishwarshafin / pepper

PEPPER-Margin-DeepVariant
MIT License
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g.vcf #181

Closed shinlin77 closed 1 year ago

shinlin77 commented 1 year ago

The output of my run was

chr1 2123373 . T 0 . END=2123373 GT:GQ:MIN_DP:PL ./.:0:24:719,72,0 chr1 2123374 . G 0 . END=2123374 GT:GQ:MIN_DP:PL ./.:0:26:101,0,521 chr1 2123375 . T 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 1 year ago

GATK still doesn't like it but the END= isn't the issue.