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Haplotype caller BP_RESOLUTION :More AD values than alleles called for
My intention is to find different bases called in a particular chromosome location irrespective of it being assigned as SNP/badbase. I user the below command:
java -jar 3.5/GenomeAnalysisTK.jar -T HaplotypeCaller -R Reference.fa -I Sample1.bam -o Sample1.BPR.vcf -ERC BP_RESOLUTION -L 1
I got my intended result but is confused with the result for example:
1 1222274 . A . . . GT:AD:DP:GQ:PL 0/0:92,1:93:99:0,120,1800
1 8333303 . A AG,AT,G,T, 0 . BaseQRankSum=0.913;ClippingRankSum=-0.141;DP=57;ExcessHet=3.0103;MLEAC=0,0,0,0,0;MLEAF=0.00,0.00,0.00,0.00,0.00;MQRankSum=0.445;RAW_MQ=205200.00;ReadPosRankSum=-0.85GT:AD:DP:GQ:PL:SB 0/0:39,2,5,2,2,0:50:36:0,79,1151,36,1041,1086,88,985,919,1611,88,985,919,1546,1611,110,942,900,957,957,928:10,29,3,8
Why there are more values for AD than the number of Alleles called for. Please note I am working with RNAseq dataset after BQSR