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.
Does BaseRecalibrator require a vcf file ?
I am following the gatk best practices guide, and using the 2 stages BaseRecalibrator process. The first recalibration is going well, the second one, produces an error like described below, I find it strange since it is not mentioned in the documentation (neither the tutorials that BaseRecalibrator require a vcf input
Here is my command
java -Xmx2g -jar GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R GRCh37-lite.fa \ -I SA495-Tumor.sorted.realigned.bam \ -BQSR SA495-Tumor.sorted.realigned.grp \ -o SA495-Tumor.sorted.post_recal.grp2
here is the error message
INFO 14:03:38,425 GATKRunReport - Uploaded run statistics report to AWS S3 ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions http://www.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid command line: This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.
Any idea ?