GATK HaplotypeCaller MNP output problem.

SkyWarriorSkyWarrior TurkeyMember ✭✭✭
edited December 2018 in Ask the GATK team

Hi
I have a situation here where a clear MNP is not literally emitted by the HaplotypeCaller engine.

The top VCF is where MNP distance is 0 and the bottom is 5. Looks like GATK HC engine is too INDEL centric for this kind of situations where it prefers emitting a GC deletion and an AA insertion rather than TGC - AAT substitution. I am wondering if this could be related to the pairHMM and its limitations in certain transitions (Not allowing 1 transversion and 2 transitions at the same time at the expense of introducing gaps in both sequences) types. And if that's the case I am also wondering if an alternative engine may also be implemented in GATK that does not rely on pairHMM only to detect sequence differences.

I can submit snippets of this if you would like to check.

Thanks.

Best Answers

  • SkyWarriorSkyWarrior Turkey ✭✭✭
    Accepted Answer

    Thanks for the detailed response. Second paragraph was exactly my thoughts so it is confirmed. I am not too agitated to get this MNP by default since seeing a weird pattern in VCF already tells me to look there manually.

    I will look forward to hearing any developments in this matter.

    Thanks again.

Answers

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @SkyWarrior What version are you using? An improvement from 4.0.5.2 -- we realize that our default Smith-Waterman parameters for aligning reads to their best haplotype was taken blindly from evolutionary models of sequence divergence, which have nothing to do with the error probabilities of sequencers -- might address this Previously the engine was sometimes favoring indels over SNPs.

    Just to be clear, are your vcfs generated by HaplotypeCaller with --max-mnp-distance 0 (default) and --max-mnp-distance 5?

    If the issue remains, could you post an IGV image of the bamout with --max-mnp-distance 5 here? After that we can proceed to examining bam snippets if we need to.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited December 2018

    This was called by GATK 4.0.11.0.

    here are the bamout images.

    Top is the --max-mnp-distance 0 and bottom is 5.

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    Apologies for not saying this earlier: could you also show all the artificial haplotypes in the bamout?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Sure here they are.

    These 2 bamouts were generated with ALL_POSSIBLE_HAPLOTYPES option. They go with the same order.

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @SkyWarrior I don't have an answer yet. Could you post a bam snippet with a padding of 1000 bp on either side?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    Sure I will.

    This is mapped to hs37d5 from 1000G.

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    Accepted Answer

    Thanks for the detailed response. Second paragraph was exactly my thoughts so it is confirmed. I am not too agitated to get this MNP by default since seeing a weird pattern in VCF already tells me to look there manually.

    I will look forward to hearing any developments in this matter.

    Thanks again.

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