This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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,