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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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Merging and variant loss #292

Open Fred-07 opened 1 year ago

Fred-07 commented 1 year ago

Hello,

Using Deepvariant v1.5 + GLnexus v1.4.3 on WES data, the variant G>C is not kept from the gvcf file. It is the same result if GLnexus model is set to "DeepVariant" or "DeepVariant_unfiltered". Twelve files are merged. The variant is found in 3 of them. The genomic region looks clean (no low mapping qual). It is not clear to me. Could you please comment about this variant?

Thanks

S4.deepvariant.wes.gvcf.gz:19       39971432        .       G       C,<*>   54.4    PASS    .  GT:GQ:DP:AD:VAF:PL       0/1:49:118:61,57,0:0.483051,0:54,0,51,990,990,990
S0.deepvariant.wes.gvcf.gz:19       39971432        .       G       C,<*>   54.7    PASS    .  GT:GQ:DP:AD:VAF:PL       0/1:47:101:37,64,0:0.633663,0:54,0,47,990,990,990
S6.deepvariant.wes.gvcf.gz:19       39971432        .       G       C,<*>   49.9    PASS    .  GT:GQ:DP:AD:VAF:PL       0/1:48:82:48,34,0:0.414634,0:49,0,54,990,990,990

Genome=hg19