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Problem with BaseRecalibration and --known-sites resource bundle file

sanzick1sanzick1 MontanaMember
edited July 2019 in Ask the GATK team

I'm using gatk-package-4.1.2.0 and java 1.8.0 and am having a problem running BaseRecalibration, following GATK best practices. The known sites files were downloaded from the gatk resource bundle. My code is as follows (note: included only one known-sites file for demonstrative purposes only):

gatk BaseRecalibrator -I alignments/6711_dedup_sorted.bam -R /gs1/RTS/NextGen/ngs_dbs/vertebrate/Homo_sapiens/gatk_bundle_hg38/Homo_sapiens_assembly38.fasta --known-sites /gs1/RTS/NextGen/ngs_dbs/vertebrate/Homo_sapiens/gatk_bundle_hg38/dbsnp_146.hg38.vcf -O data/6711_recal_data.table

And here is the error message:

A USER ERROR has occurred: Input /gs1/RTS/NextGen/ngs_dbs/vertebrate/Homo_sapiens/gatk_bundle_hg38/dbsnp_146.hg38.vcf must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

According to previous user suggestions, I unzipped the known sites vcf file, zipped it and then indexed with IndexFeatureFile. This did not solve the error. Any advice is greatly appreciated.

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @sanzick1
    Are you referring to this recommendation? So you successfully created the index and you got the same error twice? I am wondering if the tool isn't able to find the index. Let me talk to some teammates to figure out how we can best proceed to help you. PS: here is a similar post I found when searching if it is at all useful.

  • sanzick1sanzick1 MontanaMember

    Thanks. Yes, the recommendation you list is what I was referring to. I found a fix by re-downloading the files from the resource bundle, so I think it may have been something to do with the file transfer/download. Perhaps it might be useful to have a checksum file included in the resource bundles. Many thanks for your response.

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Thanks for the suggestion. I am glad you were able to get this working!

    Have a good day!

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