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.
No mutect output for certain intervals - Any idea why?
I ran mutect on certain specific intervals e.g :- chr1:40505653-40505653, chr1:139897149-139897149, chr1:198760696-198760696, etc.
However, it does not print any output for such intervals (whether it is REJECT or KEEP).
I also checked my tumor bam file to see if any genotype exists using "samtools mpileup". And it does show the genotype as well as mutation for those intervals.
Any idea why could the reason for this? I would really appreciate some information on this.