help/collaboration with mapping/variant calling pipeline

Follow

Vincenzo Landi

• March 24, 2024 10:38

Hello everyone, I need to perform alignment, mapping, and variant calling from a set of ovine (Ovis aries) genomic sequences for later use in a selection signature study. I have access to a server with good computing capabilities, but I have little experience in setting up and using pipelines for this preparatory part of the sequences. I am looking for someone who is interested in collaborating to install and use an appropriate pipeline on my server. Thank you.

0

• 

  Gökalp Çelik

  • March 29, 2024 19:09

  Hi Vincenzo Landi

  We recommend setting up workflows with the help of local IT that you may have access to. We have brief documentation of how to get started with GATK.

  https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices 

  https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 

  Once you are set there are many resources that you can use within our WARP pages that you can use to setup your own workflows. 

  https://broadinstitute.github.io/warp/ 

  Regards. 

  0

  Comment actions Permalink

Please sign in to leave a comment.