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.



  • shleeshlee CambridgeMember, Broadie, Moderator admin
    edited March 2018

    Hi @zgtman,

    Can you post the exact command you are using? Also is your intervals list 0-based indexed with .bed extension or 1-based indexed with .intervals extension? Be sure the extension is correctly specified for the type of intervals you are using.

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