Brent Pedersen

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

cyvcf2. cython + htslib == fast VCF and BCF processing

vcfanno. annotate a VCF with other VCFs/BEDs/tabixed files

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

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

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

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

bio-playground. miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

echtvar. using all the bits for echt rapid variant annotation and filtering

bwa-meth. fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

hts-nim. nim wrapper for htslib for parsing genomics data files

peddy. genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

gargs. better(?) xargs in go

cruzdb. python access to UCSC genomes database

jigv. igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

duphold. don't get DUP'ed or DEL'ed by your putative SVs.

combat.py. python / numpy / pandas / patsy version of ComBat for removing batch effects.

intintmap. fast int64-int64 map for go

slurmpy. submit jobs to slurm with quick-and-dirty python

vcfexpress. expressions on VCFs

pyfasta. fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

vcfgo. a golang library to read, write and manipulate files in the variant call format.

fishers_exact_test. Fishers Exact Test for Python (Cython)

rare-disease-wf. (WIP) best-practices workflow for rare disease

xopen. open files for buffered reading and writing in #golang

interlap. fast, pure-python interval overlap testing

seqcover. seqcover allows users to view coverage for hundreds of genes and dozens of samples

hts-nim-tools. useful command-line tools written to showcase hts-nim

combined-pvalues. combining p-values using modified stouffer-liptak for spatially correlated results (probes)

hts-python. pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

go-chartjs. golang library to make https://chartjs.org/ plots (this is vanilla #golang, not gopherjs)

irelate. Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang

bsub. python wrapper to submit jobs to bsub (and later qsub)

tiwih. simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

bigly. a pileup library that embraces the huge

align. sequence alignment. global, local, glocal.

cigar. simple library for dealing with SAM cigar strings

indelope. find large indels (in the blind spot between GATK/freebayes and SV callers)

450k-analysis-guide. A Practical (And Opinionated) Guide To Analyzing 450K Data

gsort. sort genomic data

fraguracy. overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites

geneimpacts. prioritize effects of variant annotations from VEP, SnpEff, et al.

poverlap. significance testing over interval overlaps

pybloomfaster. fast bloomfilter

bigwig-nim. command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig