Question about FS score

MadhuMadhu United StatesPosts: 9Member
edited September 2013 in Ask the GATK team

Hello,

I have the following variant called by Unified Genotyper (GATK version : GenomeAnalysisTK-2.6-5) :

chr9 139413211 . T G 7.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.913;DP=296;Dels=0.00;FS=37.414;HaplotypeScore=22.3462;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=0.508;QD=0.03;ReadPosRankSum=-3.354 GT:AD:DP:GQ:PL 0/1:180,115:282:35:35,0,3884

The FS score is 37.414. But a closer look at the bam file indicates that the 115 reads supporting alternate allele G are all in + strand. Shouldn't the FS score be much higher for this variant? 113 reads reads supporting the reference allele T at this position are in + strand and 67 are in - strand.

Please help me understand if I am wrong about my understanding of FS score or if this is a bug.

Post edited by Madhu on

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