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GATK4 on exome seqeunecing


I am interested in using the WDL pipeline available in the GATK workflow github to run GATK4 an exome data, and I have a few questions:

  1. I have noticed that the notes regarding gatk4-germline-snps-indels pipeline states that it has not been tested on exome data. Is there some pipeline that is most suitable for WES data ?

  2. I understand (as explained here) that I need to adjust the interval list. Can I simply pass a bed file with the relevant exome's kit target regions as the scattered_calling_intervals_list argument of the workflow or is there another way to do this ?

  3. Are then any other adjustments that I should consider in light the fact that I'm analysing exome data? I have looked at this thread: https://gatkforums.broadinstitute.org/gatk/discussion/6894/gatk-best-practices-for-exome-targeted-capture-small-region but it is a little bit old (that is, pre-GATK4). Are them some consideration specific to GATK4 that I should be aware of ?

Thanks in advance

Best Answers

  • dolevrdolevr
    Accepted Answer


  • dolevrdolevr Member
    Accepted Answer
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