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.

Does BaseRecalibrator require a vcf file ?

RadRad CAMember


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 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 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 Visit our website and forum for extensive documentation and answers to
 ERROR commonly asked questions
 ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
 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 ?



Best Answer


Sign In or Register to comment.