This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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.