genome

bam-readcount

Count bases in BAM/CRAM files

sciclone

An R package for inferring the subclonal architecture of tumors

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

genome

Core modules used by the GMS

bfx-workshop

A course on genomics and bioinformatics from WU

scrna_mutations

Supplementary data for Petti, et al 2019 scRNA mutation publication

qc-analysis-pipeline

Workflow used for WGS/WES data QC

fpfilter-tool

AGFusion

Python package to annotate and visualize gene fusions.

bmm

R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions

docker-bam_readcount_helper-cwl

UR

Rich Transactional Objects for Perl

cle-myeloseqhd

cle

Repo for cle related software

cle-myeloseq

Repo for cle myeloseq/haloplex assay

docker-samtools-cwl

qc-metric-aggregator

Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

docker-mapq0-filter

filter a vcf for variants with high percentage of mapq0 reads

cig-pipelines

Workflows and resources for running pipelines for somatic mutation discovery in pangenomes plus miscellaneous tools..

docker-bam-readcount

Docker containerization for "bam-readcount"

docker-cnvkit

docker-fastqc-cwl

docker-homer

fork of the quay.io homer image, moving annotations to my hardcoded link

docker-immuno_tools-cwl

docker-samtools

Docker container for Samtools

docker-somatic-llr-filter

Container for the somatic-llr filter

docker-vep_helper-cwl

hic-pipeline

HiC uniform processing pipeline

snvstory

Rapid and accurate ancestry inference using SNVs.

spectacle