If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Frequently Asked Questions - Specific Errors
1. SVGenotyper ERROR MESSAGE: Please invoke this walker with -BTI
This can be caused by an incorrect invocation of the command or a malformed input file.
The SVGenotyper walker requires the GATK
-BTI argument, specifying the ROD which contains the input VCF file. Typically something like this:
-BTI input -B:input,VCF my_input_file.vcf
Another problem that can cause this same symptom is a malformed VCF input file. For example, if you have spaces instead of tabs in the VCF file, the GATK can fail to parse the VCF file and it can cause this error.
2. SVGenotyper ERROR MESSAGE: net.sf.picard.PicardException: Malformed query; start point 59152350 lies after end point 59128983
This can be caused by a malformed VCF file where the POS field is larger than the length of the chromosome. The "end point" value is the length of the chromosome.