If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Problem with BaseRecalibration and --known-sites resource bundle file
I'm using gatk-package-188.8.131.52 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.