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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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Invalid: allele is not a DNA sequence #299

Open bartcharbon opened 8 months ago

bartcharbon commented 8 months ago

Hi,

I'm getting the following error when trying to joint call some gVCF files:

[14707] [2023-11-09 18:40:20.654] [GLnexus] [error] mother_snv.g.vcf.gz Invalid: allele is not a DNA sequence  (mother_snv.g.vcf.gz <*> chr1:16532574-16532574)
[14707] [2023-11-09 18:40:21.165] [GLnexus] [error] Failed to bulk load into DB: Failure: One or more gVCF inputs failed validation or database loading; check log for details.

variants on this position:

chr1    16532574 .       TA      TAA,<*> 1.5     RefCall AN=0;AC=0,0     GT:GQ:DP:AD:VAF:PL      ./.:5:21:6,2,0:0.0952381,0:0,3,35,990,990,990
chr1    16532574 .       TA      TAAA,<*>,T      8       PASS    AN=2;AC=1,0,0   GT:GQ:DP:AD:VAF:PL      0/1:3:21:6,5,0,4:0.238095,0,0.190476:4,0,38,990,990,990,1,13,990,35
chr1    16532574 .       T       TAA,<*> 14.7    PASS    AN=2;AC=1,0     GT:GQ:DP:AD:VAF:PL      0/1:15:21:6,5,0:0.238095,0:14,0,43,990,990,990

I have some trouble finding out what is wrong with these variants, the <*> should not be the problem I assume since it is "standard" for DeepVariant