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PhaseByTransmission in GATK4 unavailable?

serhat_tserhat_t TurkeyMember

Hi,

Is PhaseByTransmission (PBT) not available in GATK4, because I cannot see it?

Is there a reason why it is not available, e.g. not up to Broad's standards, currently being developed, or abandoned for good in GATK4?

Thanks!

Serhat

Answers

  • serhat_tserhat_t TurkeyMember

    Looking at the formula in the genotype refinement workflow (the last section named Calculation of Family Priors, CalculateGenotypePosteriors tool seems to be doing a similar (or the same?) calculation as Phase By Transmission (see the PBT paper here). If that's the case, does this mean the PBT is no longer needed?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @serhat_t
    Hi,

    Looking at the formula in the genotype refinement workflow (the last section named Calculation of Family Priors, CalculateGenotypePosteriors tool seems to be doing a similar (or the same?) calculation as Phase By Transmission (see the PBT paper here). If that's the case, does this mean the PBT is no longer needed?

    Yes, that is basically it. PhaseByTransmission is redundant in the workflow. If you do a search on the forum for the tool, you should find some other relevant threads :smile:

    -Sheila

  • serhat_tserhat_t TurkeyMember

    Hi @Sheila,

    I have a problem with using CalculateGenotypePosteriors and VariantAnnotator tools. First, I run CalculateGenotypePosteriors on a VCF file of a jointly called trio (mother, father, child). I can see the relevant annotations in the output VCF (JL, JP, PP annotations). Here is the command line:

    gatk CalculateGenotypePosteriors -V chr22only.vcf.gz -ped trio.ped -O cgp_out.vcf --de-novo-prior 1.5e-8

    Then I input the resultant VCF into VariantAnnotator to annotate the possible de novo mutations. Here is the command line:
    gatk VariantAnnotator -V cgp_out.vcf -A PossibleDeNovo -O cgp_out_annotated.vcf

    GATK rightfully throws the following warning:
    WARN PossibleDeNovo - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.

    Then I use the following command line:
    gatk VariantAnnotator -V cgp_out.vcf -A PossibleDeNovo -O cgp_out_annotated.vcf -ped trio.ped
    which returns this error:
    A USER ERROR has occurred: p is not a recognized option

    If I use --ped as the argument, gatk again says that ped is not a recognized option.

    It appears to me that VariantAnnotator cannot take in a pedigree file although it is supposed to. Could you please let me know if there is anything I am missing here? Also, pedigree file input also seems to be not defined in the help.

    Best,

    Serhat

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @serhat_t
    Hi Serhat,

    Is there an error message at the end of VariantAnnotator, or are there just WARN statements? Can you try letting the tool run to completion and check if the de novos are actually annotated?

    Thanks,
    Sheila

  • merajmeraj IndiaMember

    @serhat_t said:
    Hi @Sheila,

    I have a problem with using CalculateGenotypePosteriors and VariantAnnotator tools. First, I run CalculateGenotypePosteriors on a VCF file of a jointly called trio (mother, father, child). I can see the relevant annotations in the output VCF (JL, JP, PP annotations). Here is the command line:

    gatk CalculateGenotypePosteriors -V chr22only.vcf.gz -ped trio.ped -O cgp_out.vcf --de-novo-prior 1.5e-8

    Then I input the resultant VCF into VariantAnnotator to annotate the possible de novo mutations. Here is the command line:
    gatk VariantAnnotator -V cgp_out.vcf -A PossibleDeNovo -O cgp_out_annotated.vcf

    GATK rightfully throws the following warning:
    WARN PossibleDeNovo - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.

    Then I use the following command line:
    gatk VariantAnnotator -V cgp_out.vcf -A PossibleDeNovo -O cgp_out_annotated.vcf -ped trio.ped
    which returns this error:
    A USER ERROR has occurred: p is not a recognized option

    If I use --ped as the argument, gatk again says that ped is not a recognized option.

    It appears to me that VariantAnnotator cannot take in a pedigree file although it is supposed to. Could you please let me know if there is anything I am missing here? Also, pedigree file input also seems to be not defined in the help.

    Best,

    Serhat

    Hi,
    I am also getting the same error. Any solutions?

    Thanks in advance.
    Best wishes,
    Meraj

  • manolismanolis Member ✭✭

    Hi,

    you have to wait the official team answer but in the middle time maybe this help thread . I had the same warning and I'm using the GATK3.8 VariantAnnotator now.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @meraj, @manolis is correct, this seems to be a [known bug](I found reference to this on the github, https://github.com/broadinstitute/gatk/issues/4604).

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @meraj, @shlee let me know that there is a workaround found here

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