brentp
Doing genomics
Funding Links: https://github.com/sponsors/brentp
- Name: Brent Pedersen
- Location: Oregon, USA
- Kind: user
- Followers: 1365
- Following: 262
- Total stars: 5861
- Repositories count: 219
- Created at: 2022-11-02T17:13:24.678Z
- Updated at: 2025-03-28T11:52:31.064Z
- Last synced at: 2025-03-28T11:52:31.063Z
GitHub Sponsors Profile
I develop and maintain several tools in (moderately) wide use in genomics. Some popular packages include:
peddy and somalier for finding relatedness in cohorts
slivar for variant annotation and filtering with javascript expressions. these expressions are flexible enough to allow finding de novo, compound-het, recessive, etc variants across families.
mosdepth for rapid depth calculation
cyvcf2 for fast VCF parsing and manipulation in python.
vcfanno annotate a VCF with other VCFs or beds using a config file to indicate how fields are extracted and added.
echtvar for rapid variant annotation with allele frequency
slivar for applying simple expressions for filtering variants in trios and families.
- Current Sponsors: 3
- Past Sponsors: 0
- Total Sponsors: 3
- Minimum Sponsorship: $1.00
Featured Works
brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language: Nim - Stars: 732brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Language: Go - Stars: 371brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Language: Go - Stars: 248brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language: Nim - Stars: 277brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
Language: Nim - Stars: 259brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
Language: Rust - Stars: 150Active Sponsors
Past Sponsors
rugardo
cronooss
zykap
Sponsor Breakdown
- Unknown: 3
Past Sponsorships
View All
kortschak
davidhewitt
Sponsorship Breakdown by Kind
- User: 2