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.
Best,
Paul.