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.
SplitNCigarReads: Hard clipping of overhangs
Running SplitNCigarReads doesn't seem to hard-clip intronic overhangs despite using aggressive clipping parameters
I ran gatk (version: 220.127.116.11) with the following command
gatk SplitNCigarReads -R /path/to/genome/hg19.fa -I /path/to/$inputbam --max-mismatches-in-overhang 0 --max-bases-in-overhang 5 -O $outbam
I'm assuming the exon boundaries are inferred. if not, is there an option to provide transcript annotations to SplitNCigarReads.