I was expecting BaseCountsBySample to give the number of A, C, G and T bases at the position given by the POS column, but it seems like this is not the case. I have run HaplotypeCaller (version 3.6-0-g89b7209) on a single sample, and the BCS values returned with the BaseCountsBySample annotation are much higher than I was expecting. For example, I have an A/C SNP and the AD values are 0,30,0. I was expecting the BCS values to be something like 0,30,0,0 (or possibly slightly higher), but the values I got were 1105,251,345,1183. Are these numbers perhaps the counts of bases at all positions in all reads that cover the given position?
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