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@brentp

Brent Pedersen

brentp
Oregon

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.

@RugarDo
@Cronooss
@Zykap

Featured work

  1. brentp/mosdepth

    fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

    Nim 704
  2. brentp/vcfanno

    annotate a VCF with other VCFs/BEDs/tabixed files

    Go 367
  3. brentp/smoove

    structural variant calling and genotyping with existing tools, but, smoothly.

    Go 239
  4. brentp/somalier

    fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

    Nim 272
  5. brentp/slivar

    genetic variant expressions, annotation, and filtering for great good.

    Nim 252
  6. brentp/echtvar

    using all the bits for echt rapid variant annotation and filtering

    Rust 147

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