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Organizations

@quinlan-lab

Pinned repositories

  1. vcfanno

    annotate a VCF with other VCFs/BEDs/tabixed files

    Go 163 27

  2. xopen

    open files for buffered reading and writing in #golang

    Go 42 4

  3. gargs

    better(?) xargs in go

    Go 53 4

  4. mosdepth

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

    Nim 150 30

  5. goleft

    goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

    Go 113 13

  6. hts-nim

    nim wrapper for htslib for parsing genomics data files

    Nim 68 10

997 contributions in the last year

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Contribution activity

September 2018

Created a pull request in hall-lab/svtyper that received 3 comments

improve svtyper speed by ~30%

avoids use of CRAM sequence and base-quals which otherwise do not need to be decoded. This changes the run-time of one test-case from 20.8 seconds …

+6 −2 3 comments

Created an issue in brentp/duphold that received 3 comments

BND enhancements

if the read orientations do not match a traditional variant, then lumpy will report 2 BND elements. duphold should check if 2 BND elements are with…

3 comments

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