Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

-L option file formats

tommycarstensentommycarstensen Posts: 106Member
edited April 2013 in Ask the GATK team

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: http://gatkforums.broadinstitute.org/discussion/2219/l-option

Thanks a lot.

Also, the error message does not mention support for vcf files, but the documentation does. Are vcf files supported?

Post edited by tommycarstensen on

Best Answer

Answers

Sign In or Register to comment.