Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

-L option file formats

tommycarstensentommycarstensen Posts: 49Member
edited April 2013 in Ask the 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

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