-maxAltAlleles argument ignored in HC and genotypeGVCFs in GATK-3.7?

Hi there
I have a similiar issue as described here:
http://gatkforums.broadinstitute.org/gatk/discussion/5111/haplotypecaller-pooled-sequence-problem

I am using GATK version 3.7-0-gcfedb67 on poolseq data. I have 60 chromosomes per pool and calculated that the maximum genotype count should be 31470 when considering 3 alternate alleles.
The combination of -maxGT 31470 -maxNumPLValues 31470 -maxAltAlleles 3 works fine in HaplotypeCaller. However, running those output gvcfs in genotypeGVCFs with the same parameters I receive this error:

ERROR MESSAGE: the number of genotypes is too large for ploidy 60 and allele 9: approx. 7392009768

The programme considers 9 alleles although I have set -maxAltAlleles 3 explicitly, which should be 5 alleles including the reference and symbolic non-ref allele.

Any ideas why this is happening or tips how I can fix this?

thanks
christian

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sailerc
    Hi Christian,

    I may need you to submit a bug report. First, can you confirm this happens with the latest nightly build?

    Thanks,
    Sheila

  • sailercsailerc JICMember

    Hi Sheila,
    Thank you for the response. I just ran a small region with the latest nightly build (nightly-2017-06-07-g54ff871, version 3.7-0-gcfedb67) and obtained the same error.
    I prepared the folder for the bug report and will continue to try to login and upload the folder.
    christian

  • sailercsailerc JICMember

    Hi there
    I am trying to log into the server to upload my bug report as described in Article#1894 but was unable to do so for several days. Any other possibilities to submit the bug report?
    christian

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sailerc
    Hi Christian,

    Hmm. Sorry you are having such trouble. Can you try a few more times? If it does not work (are you getting a "time out" error?), is the folder small enough to upload to this thread?

    Thanks,
    Sheila

  • sailercsailerc JICMember

    Hi Sheila,
    I am getting this error
    530 Sorry, max 20 users -- try again later
    Yesterday I could log in but when I wanted to move the file over, I was asked for the pw again and was kicked out. My tarzipped file might also be too big, 1.1GB as I had to add our reference fasta file.
    christian

  • sailercsailerc JICMember

    Hi Sheila
    I uploaded my bug report:
    sailerc_maxAltAlleles.tar.gz

    christian

    Issue · Github
    by Sheila

    Issue Number
    2163
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    chandrans
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sailerc
    Hi Christian,

    Yes, I see a few other users had issues that were resolved today. Sorry for the trouble, but thanks for submitting! I think we are moving to a new system for bug reports, but I am not sure when it will be ready for use.

    I will have a look soon.

    -Sheila

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