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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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error #287

Open shinlin77 opened 1 year ago

shinlin77 commented 1 year ago

I got this error

[912] [2023-03-18 17:00:50.893] [GLnexus] [error] Failed to genotype: Invalid: genotyper: unexpected result when fetching record FORMAT field (W149 <0>:180392281-180392281 PL vector length 5, expected 6)

chr1 180392281 . G A,<*> 0.4 NoCall . GT:GQ:DP:AD:VAF:PL ./.:0:19:0,0,0:0,0:0,0,990,990,990

I can see why it expects 6 values, but all NoCall positions from DeepVariant look this, I believe.

wharvey31 commented 10 months ago

I am also experiencing this error. To add more context, these are occurring when attempting to merge gVCFs from DeepVariant PEPPER. These seem to be a different format than normal gVCFs in that they have a variant call for each base position as opposed to some collapsed variants.

SophieS9 commented 7 months ago

Hi @shinlin77 and @wharvey31 did either of you make progress with this issue? I've encountered the same issue when trying to merge gVCFs from DeepVariant PEPPER.

wharvey31 commented 7 months ago

@SophieS9 We ended up filtering out this variant out of the input gvcf. It was really only one or two genome-wide.