README
¶
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
Documentation
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Source Files
Directories
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| Path | Synopsis |
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cmd
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Package cnveval provides a way to evalute CNVs based on a truth-set.
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Package cnveval provides a way to evalute CNVs based on a truth-set. |
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scalers
Package scalers holds the interface for scaling depths to standardized scores.
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Package scalers holds the interface for scaling depths to standardized scores. |
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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.
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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. |
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Package depthwed combines files from goleft depth into matrices.
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Package depthwed combines files from goleft depth into matrices. |
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Package emdepth uses a simplified EM algorithm to assign copy-number given a set of depths.
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Package emdepth uses a simplified EM algorithm to assign copy-number given a set of depths. |
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mops
Package mops implements the EM algorithm described in the cn.mops paper.
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Package mops implements the EM algorithm described in the cn.mops paper. |
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Package indexsplit is used to quickly generate evenly sized (by amount of data) regions across a cohort.
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Package indexsplit is used to quickly generate evenly sized (by amount of data) regions across a cohort. |
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