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SplitNCigarReads: Hard clipping of overhangs
Running SplitNCigarReads doesn't seem to hard-clip intronic overhangs despite using aggressive clipping parameters
I ran gatk (version: 18.104.22.168) 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.