ExomeSingleSample wdl

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Sheryl

• June 08, 2023 02:07

I'm trying to run the ExomeSingleSample wdl but for hg19 or GRCh37.

I can't find any resources for this version e.g contam.exome_calling_regions.v1.UD, contam.exome_calling_regions.v1.bed,  contam.exome_calling_regions.v1.mu, exome_calling_regions.v1.interval_list, exome_evaluation_regions.v1.interval_list, Homo_sapiens_assembly38.haplotype_database.txt

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  Laura Gauthier

  • June 15, 2023 14:21

  Hi Sheryl,

  We do have a GRCh37 set of those files in the same gs://gcp-public-data--broad-references bucket, but at a slightly different path: gs://gcp-public-data--broad-references/hg19/v0. I see the contamination resources, but I don't see the exome lists.  You can use Picard'sLiftOverIntervallist (you can run it from GATK) to lift the hg38 versions back to hg19:

  java -jar gatk.jar LiftOverIntervalList \
  I=input.interval_list \
  O=output.interval_list \
  SD=hg38_reference_sequence.dict \
  CHAIN=build.chain

    You can get the chain file from 

   wget --timestamping 
          'ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz' 
          -O hg38ToHg19.over.chain.gz

  I believe that you'll need to remove the 'chr' prefix from the hg19 target contig names for everything to get along with the other Broad GRCh37 resources. 

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