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NoCall with missing PL value

See original GitHub issue

Hi,

I am using Pepper-MARGIN-DeepVariant r0.7 with custom made models for Pepper-SNP, Pepper-HP and DeepVariant. As far as I know, this release uses DeepVariant 1.2.

I have run this pipeline successfully for a small cohort of about 100 genomes but when merging the GVCF files, GLnexus 1.4.1 (with config DeepVariant) complains that at least one variant is missing PL values. I tracked down the issue to one GVCF were the record is:

CHR	POS	.	A	G,<*>	9.9	NoCall	.	GT:GQ:DP:AD:VAF:PL	./.:0:5:0,0,0:0,0:0,0,990,990,990

We can see that this GVCF record has 5 PL values where there should be 6. The corresponding record in the VCF file is:

CHR POS .	A	G	9.9	refCall	.	GT:GQ:DP:AD:VAF:C	./.:0:5:0:0:DV

The VCF record indicates that the variant call was issued by DeepVariant.

Any ideas what could be the issue here?

Thank you for your help, Guillaume

Issue Analytics

State:
Created 2 years ago
Comments:15

Top GitHub Comments

1reaction

pichuancommented, Mar 21, 2022

Hi @GuillaumeHolley , yes! Please email me at pichuan@google.com

0reactions

GuillaumeHolleycommented, Apr 19, 2022

Hi @kishwarshafin,

Thanks for the feedback, I actually forgot to get back to you about this but I have indeed filtered out the NoCall for the small cohort I have after your early feedback and it indeed solved this issue.

Good luck with solving this!

Guillaume