Avatar

Layne Sadler

  • Total activity 37
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 15
  • Subscriptions 11

Activity overview

Latest activity by Layne Sadler
  • Avatar

    Layne Sadler commented,

    GATK should issue a warning when allosomes are detected without using appropriate ploidy options

  • Avatar

    Layne Sadler commented,

    This is what I see for the chrX genotypes of a randomly selected male GT:count1/1:17020/1:3711/2:14 Consider that GQ>=15 means 95% confidence --- chrY is worse because the majority are labeled het...

  • Avatar

    Layne Sadler commented,

    Make sure that vcf tools is actually applying your filters.  In high depth samples, lots of low quality variants creep in: https://www.biostars.org/p/9564606/

  • Avatar

    Layne Sadler created a post,

    Do GATK tools support Apple silicon?

    I need to purchase a new laptop. I want to upgrade to a many-cored Mac with the new Apple silicon chips for parallelism, speed, and reduced power consumption. This is especially attractive for vari...

  • Avatar

    Layne Sadler commented,

    Does HaplotypeCaller support Apple silicon?https://www.biostars.org/p/478429/#495387

  • Avatar

    Layne Sadler commented,

    Here is a table comparing Funcotator to VEP variant classifications. It's not completely 1-1 as some of the high/moderate are missing. https://docs.google.com/document/d/1Xplvq-6wNUKQWUN7hsNPu_TFdy...

  • Avatar

    Layne Sadler commented,

    Agreed that the annotations should have their own page to be more searchable

  • Avatar

    Layne Sadler commented,

    So I got this running (hope it finishes) after a few hours of troubleshooting. It would be nice to have links to information about upstream steps like generating the supplemental files like the fas...

  • Avatar

    Layne Sadler commented,

    The page in this error message does not exist """A USER ERROR has occurred: Fasta index file ... Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-us...

  • Avatar

    Layne Sadler commented,

    Error while following the annotation example verbatim:`A USER ERROR has occurred: Unrecognized annotation group name: Standard`