ReadBackedPhasing MNP phasing call

Can the tool also work on MNP other than SNP? If not, is there any plan to expand?

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Answers

  • joeljoel USAMember

    About SNP, here are two cases that the Readbackedphase tool does not make call. Can you confirm that?

    Case 1: ref is C, but variants for allele 1 is A, allele 2 is a deletion, so the alt is A,*, but the tool does not make phasing call on it.
    Case 2: ref is N (insertion), alt is C,*, one is C and the other has none, the tool does not make a phasing call on it.

    Thank you!

  • joeljoel USAMember

    But if ref is C and alt is *, RBP tool seems to be able to phase it. Basically it can make a call on the third base, so HP field is always pos-1,pos-2, but not pos-2,pos-3.

    Is that right?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    RBP was written well before the star allele was introduced and has not been significantly updated recently, so it's possible that some case figures work by happy accident while others don't. At the moment we can't provide support for it I'm afraid.

  • joeljoel USAMember

    Is there any tool within GATK package that replaces RBP? Basically we need a phasing tool which takes reference fasta file , mapped bam, and a unphased vcf file and make phasing calls. RBP seems to be a great tool for that,

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @joel
    Hi,

    No, there is no tool that replaces RBP yet. We do recommend using HaplotypeCaller, as it makes phased calls now. We only recommend using ReadBackedPhasing for merging MNPs.

    -Sheila

  • patidarrpatidarr Member

    @Geraldine_VdAuwera said:
    The tool cannot. We have some plans to write a tool that takes the output of HaplotypeCaller (which is phased but is only SNPs and Indels, non MNPs) and merge into MNPs where appropriate. But this is a low priority project and may not happen in the near future.

    Hi @Geraldine_VdAuwera , any update on such tool, which can merge the SNPs next to each other to MNP?

    Thanks,
    Rajesh

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @patidarr No update yet, sorry. I would recommend looking for other tools outside of GATK.

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