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GATK 4 missing tools

StephenParrishStephenParrish Spartanburg, South CarolinaMember

Please let me know what happened to Callable Loci; I do not see it in GATK 4's list of tools.

Thank you for your assistance.

Best Answer

Answers

  • StephenParrishStephenParrish Spartanburg, South CarolinaMember

    Sheila -

    Thank you for your reply. GATK 3.8's CallableLoci program has been very helpful when, for instance, I want to see where no coverage occurs - as well as frequency of no calls - when I analyze a BAM file's Y chromosome coverage.

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @StephenParrish
    Hi,

    We have made porting the coverage tools a higher priority. I think the plan is to have a tool that outputs what you want plus some other coverage functionalities that others may want. You can keep track of the issue here.

    -Sheila

  • StephenParrishStephenParrish Spartanburg, South CarolinaMember

    Sheila -

    Thank you for your reply. :)

  • lplenderlplender UKMember

    Hello Sheila,
    Until the coverage tools are ported, I was thinking of using CallableLoci from GATK3.8 as part of an analysis in which everything else is done with GATK4. CallableLoci seemed to me like a standalone tool that ought to work (assuming read filters etc are checked) regardless of the version of GATK used to call the SNPs, but I was worried that I might be missing something. Is your answer saying it should probably be ok to use this GATK3 tool along with a GATK4 analysis, or were you suggesting that if we want to use it we should stick with GATK3 for everything? Thanks!

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @lpender
    Hi,

    It is fine to use GATK3 tools for coverage analysis even if you use GATK4 tools for everything else. I realize this is a phase where things are still being ported over, but most tools in GATK4 still output very similar results to GATK3, so you will be fine :smiley:

    -Sheila

  • lplenderlplender UKMember

    Thanks for your reply, that's just what I wanted to hear!

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