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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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problems merging variants with DeepVariant_WES #266

Closed tbrunetti closed 2 years ago

tbrunetti commented 2 years ago

Hi,

I am trying to merge and backfill variant calls from 4 different gVCF files produced by DeepVariant WES. Only 1 out of 4 samples have this variant called:

chr19 33302293 . T G,<*> 32.5 PASS . GT:GQ:DP:AD:VAF:PL

When I try to backfill, it continously just ignores this variant and removes it. I have tried to use the DeepVariant_unfiltered config as well, and it produces the same results. If I try to use bcftools norm -m -both to split the multiallelic calls I get a formatting error. I checked the bam files of this variant for all 4 samples and it is deeply covered so not sure why it can't merge this call. Any suggestions?

I have tried the following (and changing DeepVariantWES to DeepVaraint_unfiltered):

sudo docker run -v "/input":"/input" quay.io/mlin/glnexus:v1.2.2 /usr/local/bin/glnexus_cli --config DeepVariantWES /input/sample_4_S20.g.vcf.gz /input/sample_5_S21.g.vcf.gz /input/sample_6_S22.g.vcf.gz /input/sample_7_S23.g.vcf.gz  | bcftools view - | bgzip -c >all_variants_backfilled.vcf.gz

Thanks!

tbrunetti commented 2 years ago

Nevermind, it looks like it resolves itself if you use the DeepVaraint config only (not, WES or unfiltered).