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.

Intervals to enter for whole exome sequencing data?

Hi,
I am planning to analyze somatic variants from whole exome sequencing data. How should I enter the intervals in this case to indicate whole exome/genome?

Best Answer

Answers

  • Thanks for your answer! I am assuming it will be alright to input BED file name at the '--intervals' section instead of explicitly naming every single interval? (Which is almost untenable for whole exome sequencing)

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev

    yes -- as with all GATK tools you can either specific --intervals chrom:position OR --intervals where filename is one of the supported files of intervals (e.g. BED)

Sign In or Register to comment.