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.
Not calling all sites in gvcf option (bp_resolution)
Dear GATK team, I am trying to call all possible sites in my targeted interval (BED) with
GATK HaplotypeCaller -ERC BP_RESOLUTION. But I have for example:
chr 9 134842581 . A chr 9 134842583 . C
GATK skipped position 134842582 (I have lot of skipped positions). I am assume, that size of my output VCF should be the same as my target interval (calling base-by-base)?
I am posting print-screen in IGV
. I am not sure, if I missing something in argument.
Thank you so much for any help and clarification.