ernfrid

diagnose_dups

A tool to examine duplicate read characteristics in a BAM file

cromwell_cost

estimate cost of cromwell workflow on Google

headered_split

samtools

This is the official development repository for samtools.

bioconda-recipes

Conda recipes for the bioconda channel.

oneoffs

Crummy scripts that may never be used again or may be gold! At least they're in version control.

bootstrap

ccdg-recipes

A collection of debian package creation recipes for the CCDG pipeline

cn_region_wdl

crimson

Bioinformatics tool outputs converter to JSON or YAML

cromwell_helper_scripts

cromwell_monitor

cyvcf2

cython + htslib == fast VCF parsing

diagdupfile

incomplete python scripts for plotting diagnose_dups output

docker-parrot

docker_smoove_source_build

A dockerfile for building a specific commit of smoove from source

docker_tutorial

Notes and dockerfiles from Bioinformatics workshop on 11/2/2018

firecloud-tools

Tools for use with FireCloud

golang-dev

hts-nim

nim wrapper for htslib for parsing genomics data files

laims

long-read-validation

Long-read validation of BEDPE structural variation

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

python-dev

refilter

regenotype

regenotype duplications using different priors

smoove

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

svtools

Tools for processing and analyzing structural variants.

svtyper

Bayesian genotyper for structural variants

yaps2

Yet Another Pipeline System 2 (YAPS2)