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.
IndelRealignment step: Lost of reads?
I'm using IndelRealigner tool on my BAM file and then counting the number of reads in the BAM file using
samtools stats and it turns out that in my input BAM I have 167170574 reads mapped while in the output BAM of IndelRealignment step 121608609. Is it an expected behaviour?
Thank you in advance,