https://github.com/brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
https://github.com/brentp/bpbio
bam cram genomics genomics-visualization high-throughput-sequencing structural-variation
Last synced: 3 months ago
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basepair bio: a single binary with many useful genomics subtools.
- Host: GitHub
- URL: https://github.com/brentp/bpbio
- Owner: brentp
- License: mit
- Created: 2018-10-05T16:20:34.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-07-03T18:42:26.000Z (almost 6 years ago)
- Last Synced: 2025-01-17T20:46:15.172Z (4 months ago)
- Topics: bam, cram, genomics, genomics-visualization, high-throughput-sequencing, structural-variation
- Language: Nim
- Homepage:
- Size: 96.7 KB
- Stars: 6
- Watchers: 3
- Forks: 2
- Open Issues: 4
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Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# bpbio: a single binary with a collection of sub-commands useful for genomics
+ plot-sv-vcf: create a plot that shows the number of large and small variants separated by DEL/DUP/BND/INV for a multi-sample SV VCF. (idea from @ernfrid)
## Libraries
+ countstats: get median and percentiles for integers in constant space and little time.
+ pedfile: ped (fam) file parsing and matching to VCF.
+ duko: ergonomic embedded javascript via [duktape](https://duktape.org/) and [duktape-nim](https://github.com/manguluka/duktape-nim)
+ variexpr: simple expressions for filtering and labeling VCF records e.g.: denovo:kid.alts == 1 && mom.alts == 0 && dad.alts == 0 && kid.DP > 10
## Abandoned
+ homsv: look for depth changes in self-chains or homologous regions
+ homsv-merge: merge output from homsv