ISSRseq_CreateBAMs

Overview

ISSRseq_CreateBAMs.sh creates a sequence dictionary of the reference and maps trimmed reads from each sample to the reference using BBMap. The script ultimately produces sorted BAM files with read duplicates arising from PCR or optical artifacts flagged.

Usage

DO NOT include a slash at the end of any file path.

-O [desired prefix of output directory]

-T [number of parallel processing threads -- I recommend not exceeding number of virtualized cores]

Output Files and Directories

OUTPUT_DIR

bams

bams directory contains BAM files and associated metrics files