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genotypeConcordance for GVCF file
I need to compare two gVCF file using genotypeConcordance tool. In spite of them being the same, genotypeConcordance lists one difference between them:
1 11854456 rs1801131 T G 1484.77 . DB;DP=35;MLEAC=2,0;MLEAF=1.00,0.00;MQ=60.00;MQ0=0 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,35,0:35:99:0|1:11854457_G_A:1513,105,0,1513,105,1513:0,0,14,21 1 11856348 . N G . . . GT:DP:GQ:MIN_DP:PL 0/0:45:99:38:0,102,1141
1 11854456 . T G 6189.77 . DP=141;MLEAC=2,0;MLEAF=1.00,0.00;MQ=60.00 GT:AD:DP:GQ:PGT:PID:PL:SB 1/1:0,141,0:141:99:0|1:11854457_G_A:6218,424,0,6218,424,6218:0,0,66,75 1 11856348 . N G . . . GT:DP:GQ:MIN_DP:PL 0/0:57:99:48:0,102,1800
ALLELES_MATCH EVAL_SUPERSET_TRUTH EVAL_SUBSET_TRUTH ALLELES_DO_NOT_MATCH EVAL_ONLY TRUTH_ONLY 1 0 0 0 0 1
I wonder why that is. Is there a way to run genotypeConcordance on the GVCF file?
Please note that I replaced the ref allele with 'N' and the alt allele with G (which was the ref allele) because otherwise GATK throws the error of duplicate alleles.
Any help would be appreciated.