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HaplotypeCaller gives out variants that are not present in the BAM file
I am using the last version of HaplotypeCaller on human diploid BW alignments and sometimes I find variants in the VCF file that have been called with a high quality that are simply not present in the BAM (sometime missense somtimes deletions) file (that had been duplicate removed, realigned and recalibrated before). How could I find out at what step the mistake happens.
Thanks a lot for the software and your help,