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In some of my calls, I have ID=BaseQRankSum, whereas in others, it isn't reported. I'm wondering what makes the unified genotyper call this for some SNPs but not for others. Also, in the documentation, it says this test cannot be done on homozygous sites: "bases of the alternate allele). Note that the base quality rank sum test can not be calculated for homozygous sites."
But this value is present at 1/1 sites for the GT field, which I understand it to be homozygous calls? e.g.
BaseQRankSum not called: chr1 5503270 . G A 1023.62 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=56.06;MQ0=0;QD=35.30;SB=-375.13 GT:AD:DP:GQ:PL 1/1:0,29:29:87.24:1057,87,0
BaseQRankSum called: chr1 6577241 . G A 1359.86 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.312;DP=43;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=59.13;MQ0=0;MQRankSum=1.692;QD=31.62;ReadPosRankSum=0.787;SB=-641.06 GT:AD:DP:GQ:PL 1/1:3,40:43:34.37:1393,34,0
Can someone help interpret this?
Many thanks, Ken