Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/brentp/tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

https://github.com/brentp/tiwih

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.7%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

Basic Info
  • Host: GitHub
  • Owner: brentp
  • License: mit
  • Language: Nim
  • Default Branch: main
  • Size: 70.3 KB
Statistics
  • Stars: 44
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 20
Created about 5 years ago · Last pushed about 3 years ago
Metadata Files
Readme Changelog License

README.md

tiwih: tools i wish(ed) i had

  • fairegions: (fai) generate equal length regions from an fai (for parallelization)
  • combineslivarcounts: combine counts from slivar for original call and for compound-hets
  • highcov: (bam/cram) find high-coverage regions (~3 minutes per 30X cram)
  • meandepth: (bam/cram) quickly calculate meandepth by sampling (~2 seconds)
  • samplename: (bam/cram) print sample name from readgroup tag
  • setsvalt: (vcf/bcf) set the ALT allele in a manta VCF to left + N + right for paragraph genotyper
  • setref: (vcf/bcf) change ref allele from N to the actual allele.
  • slivarsplitfam: (vcf/bcf) split joint slivar files by family and inheritance mode
  • sumslivarcounts: sum counts from slivar from same samples split across multiple files/regions
  • vcf2bedpe : convert and SV VCF to simple bedpe

Owner

  • Name: Brent Pedersen
  • Login: brentp
  • Kind: user
  • Location: Oregon, USA

Doing genomics

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • soumyarao86 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 20
proxy.golang.org: github.com/brentp/tiwih
  • Versions: 20
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.7%
Average: 5.9%
Dependent repos count: 6.1%
Last synced: 10 months ago