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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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Glnexus failed to joint the g.vcf file generated from GATK Haplotypecaller with BP_resolution #276

Open Drdreammaerd opened 2 years ago

Drdreammaerd commented 2 years ago

Hi,

I want to use glnexus after gatk haplotype caller with BP_resolution. However, it failed by giving this error message.

Message

[GLnexus] [error] Failed to genotype: Invalid: genotyper: gVCF reference depth FORMAT field is missing or malformed (CP-F0823-001U_BP_germline <0>:69270-69270 (MIN_DP))

It works well if I run the glnexus with the g.vcf derived from the halotypecaller default setting.

May I know if I should change some settings specifically for BP_resolution?

Thanks,

David