bedtk

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  "desc": "Simple toolset for BED files",
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  "full_name": "bedtk",
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  "github_last_commit_at": "2025-08-24T23:18:04Z",
  "github_readme_excerpt": "## Getting Started\n\n```sh\n# compile and install\ngit clone https://github.com/lh3/bedtk\ncd bedtk \u0026\u0026 make\n# filter a BED or VCF file\n./bedtk flt test/test-anno.bed.gz test/test-iso.bed.gz\n./bedtk flt -v test/test-anno.bed.gz test/test-iso.bed.gz      # non-overlapping lines\n./bedtk flt -cw100 test/test-anno.bed.gz test/test-sub.vcf.gz  # with a window\n# intersect (no sorting needed; overlapping records allowed)\n./bedtk isec test/test-anno.bed.gz test/test-iso.bed.gz\n# compute the breadth of coverage\n./bedtk cov test/test-anno.bed.gz test/test-iso.bed.gz\n# sort a BED file\n./bedtk sort test/test-iso.bed.gz\n./bedtk sort -s test/chr_list.txt test/test-iso.bed.gz\n# merge overlapping records (no sorting needed)\n./bedtk merge test/test-anno.bed.gz\n```\n\n## Introduction\n\nBedtk is a set of simple tools to process BED files. It so far implements\nintersection, subtraction, sorting, merging and computing the breadth of\ncoverage. Bedtk is not as versatile as [bedtools][bedtools] and never aims to\nmatch the bedtools feature set. It instead focuses on performance. Bedtk\nis several to tens of times faster and uses a fraction of memory. It also\nprovides a few convenient functions. For example, sorting, merging and\nintersection can be done in one go without Unix pipes.\n\nBedtk is published in:\n\u003e Li H and Rong J (2021) Bedtk: finding interval overlap with implicit interval tree.\n\u003e *Bioinformatics*, **37**:1315-1316\n\n[bedtools]: https://github.com/arq5x/bedtools2\n[cr]: https://github.com/lh3/cgranges\n",
  "github_repo": "lh3/bedtk",
  "github_stars": 144,
  "github_topics": [
    "bioinformatics"
  ],
  "homepage": "https://github.com/lh3/bedtk",
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  "license": "MIT",
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  "ruby_source_path": "Formula/b/bedtk.rb",
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