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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?

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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)

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