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-L option file formats

tommycarstensentommycarstensen United KingdomMember
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:

Thanks a lot.

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

Best Answer


  • tommycarstensentommycarstensen United KingdomMember

    Thanks for answering my question. Sorry for double posting. Sorry for asking a question that was already answered on the website. Thank you.

  • tommycarstensentommycarstensen United KingdomMember

    Just in case others are in doubt about the file format, this is what worked for me (.interval_list):

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