Complete this survey about your research needs and be entered to win an Amazon gift card or FireCloud credit.
Read more about it here!
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.6 is out. See the GATK4 beta page for download and details.

-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

Sign In or Register to comment.