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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:
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?

Best Answer

Answers

  • 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):
    22:51238831-51238831
    22:51238924-51238924
    22:51238983-51238983
    22:51239600-51239600
    22:51239664-51239664
    22:51239688-51239688
    22:51239696-51239696
    22:51239794-51239794
    22:51240081-51240081
    22:51240820-51240820

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