goleft

goleft is a collection of bioinformatics tools written in go distributed together as a single binary under a liberal (MIT) license.

Running the binary goleft will give a list of subcommands with a short description. Running any subcommand without arguments will give a full help for that command.

Installation

The easiest way to install goleft is to download the latest binary from the releases and make sure to chmod +x the resulting binary.

If you are using go, you can build from source with:

go get -u github.com/brentp/goleft/...
go install github.com/brentp/goleft/cmd/goleft

goleft is also available in bioconda

Commands

• covstats : estimate coverage and insert-size statistics on bams by sampling
• depth : parallelize calls to samtools in user-defined windows
• depthwed : matricize output from depth to n-sites * n-samples
• indexcov : quick coverage estimate using only the bam index
• indexsplit : generate regions of even data across a cohort (for parallelization)
• samplename: report samplename(s) from a bam's SM tag