PL field in gvcf file equal to zero

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5.2 years ago

Researcher ▴ 20

I have a genomics data from Bacteria (E. Coli.) and used GATK 4 for variant calling. I have noticed that for some samples and some loci, PL is 0,0. Can anyone please explain this?

eg. NC_000913 4473651 . C <non_ref> . . . GT:AD:DP:GQ:PL 0:2,0:2:0:0,0

How can we interpret that? becuase in this case, the GT in later steps will be "." as it will be driven from PL, when we combine and genotype the samples.

thanks in advance.

GATK BP_RESOLUTION GVCF VCF • 1.1k views

ADD COMMENT • link 5.2 years ago by Researcher ▴ 20

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there is no called genotype here: DP is 2, GQ is 0. this variant could be a node between two statistically different regions, or a variant with an ugly environment (clipping...)

ADD REPLY • link 5.2 years ago by Pierre Lindenbaum 164k

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Hi Pierre, as there is no called GT at this loci, in only some of the samples, could that means absence of a gene in those samples? Regards

ADD REPLY • link 5.2 years ago by ali.al-fatlawi ▴ 10

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Thanks for your answer, but could you please explain your answer more as I am quite new in this field and didn't understand you totally!?

ADD REPLY • link 5.2 years ago by Researcher ▴ 20

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