genome/vcf-evaluation

This repository has been archived on 31/Jan/2020
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Created almost 10 years ago
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genome/vcf-evaluation

genome

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scripts and modules to facilitate comparing gold standard VCFs

bam-readcount

Count bases in BAM/CRAM files

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

sciclone

An R package for inferring the subclonal architecture of tumors

breakdancer

SV detection from paired end reads mapping

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

Common Workflow Language

gms

The Genome Modeling System installer

genome

Core modules used by the GMS

bfx-workshop

A course on genomics and bioinformatics from WU

somatic-sniper

A tool to call somatic single nucleotide variants.

docs

joinx

a tool for processing .bed and .vcf files

scrna_mutations

Supplementary data for Petti, et al 2019 scRNA mutation publication

mendelscan

Analyze exome data for Mendelian disorders. Still in alpha-testing.

ptero

tigra-sv

sciclone-meta

accessory scripts and documentation related to the sciclone R package at genome/sciclone

rss2jira

Create JIRA issues when keywords are matched in RSS feeds.

docker-rnaseq

A fat docker image for running RnaSeq

UR

Rich Transactional Objects for Perl

bmm

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

dindel-tgi

A fork of dindel

docker-bcftools

Docker container for bcftools

docker-star

Docker container for the star aligner

docker-bam_readcount_helper-cwl

graphite

Graphite Config and Cron Scripts

ptero-lsf

Ptero services to run commands via LSF

cle-chromoseq

Repository for CLE ChromoSeq Assay

pairoscope

simple static plots of read pairing information

docker-dna-alignment

A fat docker image for running alignment

aml31Benchmarking

cle-myeloseqhd

tgi-workflow

the workflow server used at TGI

flow-core

cncwl

docker-vep-cwl

Variant of vep image without an ENTRYPOINT

cle-myeloseq

Repo for cle myeloseq/haloplex assay

docker-gossamer

Docker container for gossamer bioinformatics suite

ptero-workflow

Client-facing API for the PTero system

cle

Repo for cle related software

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-custom-clinvar-vcf

docker-samtools-cwl

ptero-petri

Petri net core of the PTero system

somatic-snv-test-data

Example Data for SomaticSniper

build-common

common build scripts used in c/c++ projects

nessy-client-perl

Perl client for the nessy-server lock daemon

nessy-server

cancer-genomics-workflow-wiki

A full featured, including pull requests, git repo for the arvados_trial Wiki

docker-fgbio

A docker image for using fgbio

docker-strelka

A docker image for Strelka