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gatk4-germline-snps-indels workflow - cannot find resources for b37

I am using https://github.com/gatk-workflows/gatk4-germline-snps-indels and have managed to run this successfully for hg38! Thanks :) This makes my life so much easier!

I now need to run this for b37. I managed to find the necessary files for the HaplotypeCaller workflow input json in the broad ftp resource bundle however, for the JointDiscovery workflow input json (https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4.hg38.wgs.inputs.json) I was not able to find the two corresponding files for b37 available for hg38:

  "##_COMMENT3": "INTERVALS",
  "JointGenotyping.eval_interval_list": "gs://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
  "JointGenotyping.unpadded_intervals_file": "gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals",

Would be a big help if you would be able to point me towards the corresponding files for b37.

Thanks so much,

Alon

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @alongalor
    Hi Alon,

    It looks like we provide an interval list here for b37.

    -Sheila

  • alongaloralongalor Member

    Hi Sheila,

    Are you referring to wgs_calling_regions.v1.interval_list? I assume this corresponds to wgs_evaluation-regions.hg38.interval_list.

    What about for hg38.even.handcurafed.20k.intervals? Is there a file for b37 that correspond to that file?

    Thanks a lot,

    Alon

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