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bedtools2

A powerful toolset for genome arithmetic.

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

caviar

cc2qe.github.io

cinid

Quantify chromosomal instability (CIN) of a tumor from genetic sequence data

cnvgram

Draw CNV diagrams

covid-19

cyvcf

A fast Python library for VCF files leveraging Cython for speed.

disktime

emerald

tools to efficiently retrieve and calculate LD

epi

epi-scripts

fvcf

gemini

a lightweight db framework for disease and population genetics.

grabix

a wee tool for random access into BGZF files.

gtex

GTEx analysis scripts

gtex_author_list

ion

File streaming and text handling tools

layertools

Smaller projects

ldscan

Genome wide scan for linkage disequilibrium

local_pca

Methods for examining PCA locally along the genome.

prime

pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

sandbox

Primordial soup of short scripts

seque

Tools for manipulating next-generation sequencing data

simu

Fast and Efficient Tool to Simulate Summary Statistics from Genome-Wide Association Studies

soccer_stats

stabilizing

svscore

Prioritize structural variants based on annotations and C scores - still under active development

svtools

Tools for processing and analyzing structural variants.