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HaplotypeCaller and downsampling
We're seeing some annotation values varying more than we would have expected when the downsample to coverage setting is adjusted. In the following example, BaseQRankSum, FS and ReadPosRankSum change a fair bit. Is this expected behavior? Any suggestions as to why this might happen?
Downsample = 250
chr19 1228412 rs142990629 AAAGCTTGGG A 3444.73 . AC=1;AF=0.500;AN=2; BaseQRankSum=-1.674; ClippingRankSum=2.617;DB;DP=514;FS=0.000; MLEAC=1; MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.059;QD=6.70;ReadPosRankSum=0.173 GT:AD:DP:GQ:PL 0/1:355,108:463:99:3482,0,36818
Downsample = 2000
chr19 1228412 rs142990629 AAAGCTTGGG A 3811.73 . AC=1; AF=0.500; AN=2; BaseQRankSum=1.395;ClippingRankSum=2.358;DB;DP=532;FS=2.961;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.443;QD=7.16;ReadPosRankSum=2.027 GT:AD:DP:GQ:PL 0/1:380,119:499:99:3849,0,39507