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GATK $5 genome pipeline fails because no suitable codecs found in dbSNP VCF index

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2 comments

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    Tiffany Miller

    Hello Cuca Dogo

    What is the name of the workspace and the submission Id?

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    Tiffany Miller

    There may be an issue with your input vcf file that BQSR doesn't like as discussed here

    Updated: This broad bucket path will soon not be available for free. Can you update the config to use these paths and run again?

    dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf

    dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx

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