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.
-L option file formats
I got this error message, when trying to use a file to specify at which positions to emit variants:
ERROR MESSAGE: Couldn't read file /lustre/scratch109/sanger/tc9/agv/wgs/pipeline/union4x.positions because The interval file /lustre/scratch109/sanger/tc9/agv/wgs/pipeline/union4x.positions does not have one of the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). Please rename your file with the appropriate extension.
Is there a GATK page describing those 5 file formats? Some of them are unknown to me; e.g. .list.
I asked my question here, but please ignore it:
Thanks a lot.
Also, the error message does not mention support for vcf files, but the documentation does. Are vcf files supported?