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GenotypeGVCFs wrongly genotypes positions spanning deletions
When we run GenotypeGVCFs without the combine step, we are getting wrong genotypes for positions spanning deletions. We are also missing the AD values for the deletion allele. For example see these calls:
1 6529182 rs375111412 TTCCTCC T,TTCC 7506.41 . AC=1,1;AF=0.009615,0.221;AN=4;BaseQRankSum=0.096;ClippingRankSum=0.292;DB;DP=3437;ExcessHet=18.9343;FS=0;InbreedingCoeff=-0.2993;MLEAC=1,23;MLEAF=0.009615,0.221;MQ=60.04;MQRankSum=0.042;QD=4.27;ReadPosRankSum=0.585;SOR=0.674 GT:AD:DP:GQ:PGT:PID:PL 0/2:165,4,22:191:99:.:.:408,769,11860,0,7242,6888 0/1:24,38,2:64:99:.:.:1513,0,1384,1504,993,2521 1 6529183 . T . . . AN=4;DP=3786 GT:AD:DP:PGT:PID:RGQ 0/0:165:191:.:.:99 0/0:24:64:.:.:99
We are using GATK 3.5. We had 52 samples in this VCF and sliced it with bcftools for easier reading.
This is the same output if we do run CombineGVCFs on the individual gVCF files first.
1 6529182 rs375111412 TTCCTCC TTCC,T 7506.41 . AC=1,1;AF=0.221,0.009615;AN=4;BaseQRankSum=0.096;ClippingRankSum=0.292;DB;DP=3437;ExcessHet=18.9343;FS=0;InbreedingCoeff=-0.2993;MLEAC=23,1;MLEAF=0.221,0.009615;MQ=60.04;MQRankSum=0.042;QD=4.27;ReadPosRankSum=0.585;SOR=0.674 GT:AD:DP:GQ:PGT:PID:PL 0/1:165,22,4:191:99:.:.:408,0,6888,769,7242,11860 0/2:24,2,38:64:99:.:.:1513,1504,2521,0,993,1384 1 6529183 . T * . . AC=0;AF=0;AN=4;DP=3786 GT:AD:DP:PGT:PID:RGQ 0/0:165,22:191:.:.:99 0/0:24,38:64:.:.:99
Should GenotypeGVCFs properly genotype positions spanning deletions? Or is running CombineGVCFs a required step?