I am having trouble interpreting the Pindel "per sample" columns of the output files. In a previous post it has been reported that 32+ data are sample Id plus 6 values indicating: 1) RefSupportingLeft 2) RefSupportingRight 3) AltSupportingLeft 4) AltSupportingLeftUnique 5) AltSupportingRight 6) AltSupportingRightUnique
and that you should take max(RefSupportingLeft, RefSupportingRight) and sum(AltSupportingLeft, AltSupportingRight) to get your genotype.
This is a bit confusing because apparently these data don't fit with what is reported in IGV (aligner is BWA). The major issue is that the number of 'reference' counts doesn't match with ref read counts shown in the viewer. Could anyone explain in detail how the RefSupportingLeft and RefSupportingRight are calculated ?