Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

ExomeSingleSample wdl


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    Laura Gauthier

    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 \

      You can get the chain file from 

     wget --timestamping 
            -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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