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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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,