EMIT_ALL_CONFIDENT_SITES for bacteria

ProtaeusProtaeus Posts: 17Member
edited October 2012 in Ask the GATK team

Hello, I am running the variant caller to identify SNPs and Reference Calls in a bacterial genome, which means I am running with -ploidy 1, -glm POOLSNP and -prnm POOL as suggested in other regions of this forum. The tool does an excellent job when just looking for Variants, but when I attempt to EMIT_ALL_CONFIDENT_SITES, it just spits out the SNPs and not the reference calls. When I remove the arguments stating that it is ploidy of 1, it works fine but calls SNPs that shouldn't be there since it's assuming diploid. Thus, I would really like to be able to emit all sites in ploidy=1 mode. Any reason why this is not possible? Thanks for you help! John

Post edited by Geraldine_VdAuwera on

Best Answer

  • delangeldelangel Posts: 71GATK Developer mod
    Answer ✓

    Hi - yes, we also just noticed that emitting confident reference sites is broken when ploidy != 2. This should be fixed in the next couple of days, I'll let you know when this is ready. Note that when you update to the newer version (2.1.x) you'll have to change your command line back to -glm SNP, the POOL* arguments have been deprecated.

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