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Germline Pipeline - Codon invalid error

ncamardancamarda DFCIMember, Broadie
edited August 2016 in Oncotator

I am struggling with the Germline Pipeline available from the Algorithm_Commons workspace on Firehose. All of the samples I am trying to process with this workflow were sequenced at the Broad, either through the CRSP or the Picard pipelines. The samples fail at the "Single Sample VCFtoMAF" step (the last step of the workflow) because each of these samples has, according to the task, an 'invalid codon'. I've attached an example of the error message below.

I've been stumped with this problem for a couple of days now, and I've talked to multiple people involved in Firehose help. Ultimately, I cannot seem to fix this problem easily without altering the task itself. Is there something wrong with my samples? Something wrong with the task itself? Has anyone else experienced this problem? Any help and/or advice would be much appreciated. Thank you!


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    This sounds like an Oncotator problem. We don't provide support for that but our colleague @LeeTL1220 may be able to help you.

  • hexyhexy ChinaMember

    I run into the same error, actually oncotator cannot annotate such MNP like:
    chr2 1842968 1842968 T A,C, so you need to split this MNP into 2 SNPs:
    chr2 1842968 1842968 T A and
    chr2 1842968 1842968 T C.
    and then oncotator could run.
    But I don't think it's the best solution. Vep annotate this MNP like this:
    * Reference_Allele is 'T',
    * Tumor_Seq_Allele1 is 'T'
    * Tumor_Seq_Allele1 is 'C'
    * Match_Norm_Seq_Allele1 is 'A'
    * Match_Norm_Seq_Allele2 is 'C'
    *IGV shows the site is an alteration from T to C.... So it may depend on the variants in Normal sample and tomor sample

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hey @hexy,

    Did you solve this issue or have a specific question?

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev

    @hexy chr2 1842968 1842968 T A,C is a multiallelic, not a MNP. If you want a multiallelic, in MAF, you would do what you did abovechr2 1842968 1842968 T A and chr2 1842968 1842968 T C.

    And your VEP results are incorrect.

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