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Remove symbolic alleles from REF in a VCF file

Hi there!

I'm trying to do BQSR on some sheep genomes. I downloaded the known variants from Ensembl and converted the GVF file to VCF using their script. However, once I try to use it to ran GATK 3.5.0 BaseRecalibrator, it propt this message:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions
##### ERROR
##### ERROR MESSAGE: Cannot tag a symbolic allele as the reference allele

I've looked for "<>" symbols, as they are the markers for symbolic alleles in VCF as far as I've read, but grep didn't found any outside of the header, and I've tried out with GATK 3.8 with the same results.

Any idea of what could be happening and how can I solve it?

Thank you for your help.


  • bshifawbshifaw Member, Broadie, Moderator admin

    You mentioned you converted their file into VCF, perhaps there's something off with the conversion. Try verifying the VCF using ValidateVariants. Also, if possible switch to gatk4.1 which often improves on earlier versions with bug fixes.

  • PedroMorellPedroMorell Member
    I validated it and looked for anything other than [ACGT] in the reference column without luck. Unluckily, I'm stuck with this version as I'm following the pipeline used to produce previous data. The only solution I've found is to choose another set of known variants and use them instead.
  • bshifawbshifaw Member, Broadie, Moderator admin

    Glad to hear you found a workaround. I'm curious, did the previous pipeline use the same known sheep variants from Ensemble?

  • PedroMorellPedroMorell Member
    I don't know. I'm reconstructing it from a verbal description, and this bit wasn't specified. I used the Ensembl file since it's the source they listed for the reference genome.
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