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?