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.
Hello, I am using ASER Read counter on WES bam files.
I provided the flag -dels asking it to include information on indels. However I see the following problem.
My input file (-sites) has a position in the reference called "CAG" and an alternate allele called "C", which means there was a deletion.
However this is present within the output from ASEReadCounter as ref allele C and alt allele also C. If I understand it correctly the -dels option is supposed to include information on indels , but that information is not being preserved in the output, the reference still shows up only as "C". Is this expected ???