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GT calls and PL values in VCF

I've been analyzing GBS data for a fungus (haploid) and I'm puzzled by some of the genotype calls I get in the VCF. For example:

GT:PL:DP:GQ ./.:0,255,255:233:99

Why is no genotype given (GT) while PL is 0,255,255? Shouldn't this position be 0/0?

From the same individual is have 0/0:0,255,224:141:99 a few positions down and another individual at the same position show 0/0:0,33,127:11:99.

I'm using VCFTools to filter the .bcf

snp sequencing
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written by arnaud.capron • arnaud.capron

1 answer

Can you paste the whole line of output? Do you see PASS or FAIL in the column for QC? Are you using a filter on high coverage?

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written by Fabio Marroni Fabio Marroni

Yep, that was the high coverage filter (--max-DP 200). Thanks!

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written by arnaud.capron • arnaud.capron

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