goleft

package module
v0.2.6 Latest Latest
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Published: Feb 14, 2024 License: MIT Imports: 0 Imported by: 0

README

goleft

Build Status

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

Documentation

Index

Constants

View Source
const Version = "0.2.6"

Variables

This section is empty.

Functions

This section is empty.

Types

This section is empty.

Directories

Path Synopsis
cmd
Package cnveval provides a way to evalute CNVs based on a truth-set.
Package cnveval provides a way to evalute CNVs based on a truth-set.
scalers
Package scalers holds the interface for scaling depths to standardized scores.
Package scalers holds the interface for scaling depths to standardized scores.
Package depth parallelizes calls to samtools depths and outputs: 1) $prefix.callable.bed that contains collapsed per-base regions of NO/LOW/or CALLABLE coverage.
Package depth parallelizes calls to samtools depths and outputs: 1) $prefix.callable.bed that contains collapsed per-base regions of NO/LOW/or CALLABLE coverage.
Package depthwed combines files from goleft depth into matrices.
Package depthwed combines files from goleft depth into matrices.
Package emdepth uses a simplified EM algorithm to assign copy-number given a set of depths.
Package emdepth uses a simplified EM algorithm to assign copy-number given a set of depths.
mops
Package mops implements the EM algorithm described in the cn.mops paper.
Package mops implements the EM algorithm described in the cn.mops paper.
Package indexsplit is used to quickly generate evenly sized (by amount of data) regions across a cohort.
Package indexsplit is used to quickly generate evenly sized (by amount of data) regions across a cohort.

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