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Bug - wrong genotype called by HaplotypeCaller
HaplotypeCaller in gatk v184.108.40.206 is giving markedly wrong genotypes in the GVCF file. See below for an example, where a locus with 17 reference reads and 33 ALT reads is being called as homozygous ALT (1/1).
This is also seen in many other loci. This must be a bug and needs to be investigated, because this would affect every GATK variant calling pipeline currently being used. Let me know what info you need and I can send it.
chr1 1482055 . G A, 1095.03 . AS_RAW_BaseQRankSum=|0.7,1|NaN;AS_RAW_MQ=28849.00|78195.00|0.00;AS_RAW_MQRankSum=|2.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.4,1|NaN;AS_SB_TABLE=16,1|32,1|0,0;BaseQRankSum=0.719;DP=50;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.107;RAW_MQandDP=107044,50;ReadPosRankSum=-1.342 GT:AD:DP:GQ:PL:SB 1/1:17,33,0:50:99:1109,99,0,1109,99,1109:16,1,32,1