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molgenis / vip

Variant Interpretation Pipeline
https://molgenis.github.io/vip/
GNU Lesser General Public License v3.0
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gVCF merge fails for haploid calls #370

Closed dennishendriksen closed 1 year ago

dennishendriksen commented 1 year ago 
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
Y       9306051 rs199532657     A       G,<NON_REF>     596.01  .       BaseQRankSum=5.368;ClippingRankSum=0.000;DB;DP=128;MLEAC=1,0;MLEAF=1.00,0.00;MQRankSum=1.568;RAW_MQ=77054.00;ReadPosRankSum=-1.749    GT:AD:DP:GQ:PL:SB       1:54,73,0:127:99:606,0,1988:3,51,2,71

[27989] [2023-05-12 11:30:30.327] [GLnexus] [error] Failed to genotype: Invalid: genotyper: unexpected result when fetching record FORMAT field (reheadered_VIP_sampleC_index_m <23>:9306051-9306051 PL vector length 3, expected 6)
dennishendriksen commented 1 year ago

See https://github.com/dnanexus-rnd/GLnexus/issues/259

dennishendriksen commented 1 year ago

Fixed in v5.5.0