Avatar

Damian Fermin

  • Total activity 8
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 3

Activity overview

Latest activity by Damian Fermin
  • Avatar

    Damian Fermin created a post,

    What is the correct step? VQSR and CNNScoreVariants?

    Answered

    I think this should be an easy one so I apologize if it's a stupid question. I'm confused from reading the Best practices workflow for Germline short variant discovery. I am trying to get a set of ...

  • Avatar

    Damian Fermin created a post,

    Should decoy chromosomes be dropped at HaplotyeCaller Step?

    Hi I am analyzing ~600 30X WGS samples using GATK 4.1.8.0 and I've finally reached the stage where I can run my recalibrated BAM files through HaplotypeCaller. I know I can speed the process up via...

  • Avatar

    Damian Fermin commented,

      So I looked at the BAM files for the sites with the stray variants. They are definitely getting a lot of reads supporting their call (some in excess of 100).  Extracting about 20 of these aligned...

  • Avatar

    Damian Fermin commented,

    Hi Derek Thanks for getting back to me.   I've checked the BAM files for each patient looking at the average read depth of the gene SRY. It's on the Y chromosome and should not have read counts for...

  • Avatar

    Damian Fermin created a post,

    Calling variants on chromosome Y

    Hello I'm trying to use GATK 4.1 to analyze WGS data I have.At this point I'm only testing and optimizing my pipeline so I am only working with 4 samples (2 males and 2 females). I've followed the ...