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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.