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HaplotypeCaller gives out variants that are not present in the BAM file

mschuemschue BerlinMember

Dear Geraldine,

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,



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Markus,

    Do you mean you don't see evidence for the variants in the reads?

    If so, try enabling display of soft-clipped reads in IGV. It may be that the evidence is there but is not displayed because soft-clips are turned off by default. If you still can't see evidence for these variants please post an example (variant record + screenshot of pileup).

  • KurtKurt Member ✭✭✭

    You can also try the --bamOutput option in HaplotypeCaller just in the region where you have a question, use the -L option to limit it to an interval, so that you can see what HaplotypeCaller is thinking.

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