Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

IndelRealigner and option -L

lindenblindenb FranceMember ✭✭

'just asking for confirmation: if I run IndelRealigner with option -L my.capture.bed does indelrealigner:

  • keep all the reads but only realign them in region of the bed ?
  • or only keep the reads in the given region (smaller BAM)?

Thanks

Best Answer

Answers

Sign In or Register to comment.