https://github.com/lh3/bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
https://github.com/lh3/bedtk

bioinformatics

Last synced: 17 days ago
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A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

• Host: GitHub
• URL: https://github.com/lh3/bedtk
• Owner: lh3
• License: mit
• Created: 2019-10-02T18:29:37.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-05-28T21:48:28.000Z (7 months ago)
• Last Synced: 2024-12-08T14:11:47.642Z (29 days ago)
• Topics: bioinformatics
• Language: C
• Homepage:
• Size: 445 KB
• Stars: 137
• Watchers: 8
• Forks: 15
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
## Getting Started

```sh

# compile and install

git clone https://github.com/lh3/bedtk

cd bedtk && make

# filter a BED or VCF file

./bedtk flt test/test-anno.bed.gz test/test-iso.bed.gz

./bedtk flt -v test/test-anno.bed.gz test/test-iso.bed.gz      # non-overlapping lines

./bedtk flt -cw100 test/test-anno.bed.gz test/test-sub.vcf.gz  # with a window

# intersect (no sorting needed; overlapping records allowed)

./bedtk isec test/test-anno.bed.gz test/test-iso.bed.gz

# compute the breadth of coverage

./bedtk cov test/test-anno.bed.gz test/test-iso.bed.gz

# sort a BED file

./bedtk sort test/test-iso.bed.gz

./bedtk sort -s test/chr_list.txt test/test-iso.bed.gz

# merge overlapping records (no sorting needed)

./bedtk merge test/test-anno.bed.gz

```

## Introduction

Bedtk is a set of simple tools to process BED files. It so far implements

intersection, subtraction, sorting, merging and computing the breadth of

coverage. Bedtk is not as versatile as [bedtools][bedtools] and never aims to

match the bedtools feature set. It instead focuses on performance. Bedtk

is several to tens of times faster and uses a fraction of memory. It also

provides a few convenient functions. For example, sorting, merging and

intersection can be done in one go without Unix pipes.

Bedtk is published in:

> Li H and Rong J (2021) Bedtk: finding interval overlap with implicit interval tree.

> *Bioinformatics*, **37**:1315-1316

[bedtools]: https://github.com/arq5x/bedtools2

[cr]: https://github.com/lh3/cgranges