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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.
3 sponsors have funded brentp’s work.
Featured work
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brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Nim 704 -
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Go 367 -
brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Go 239 -
brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Nim 272 -
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
Nim 252 -
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
Rust 147