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bam-readcount
Count bases in BAM/CRAM filespindel
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 tumorsbreakdancer
SV detection from paired end reads mappinganalysis-workflows
Open workflow definitions for genomic analysis from MGI at WUSM.gms
The Genome Modeling System installergenome
Core modules used by the GMSbfx-workshop
A course on genomics and bioinformatics from WUsomatic-sniper
A tool to call somatic single nucleotide variants.docs
joinx
a tool for processing .bed and .vcf filesscrna_mutations
Supplementary data for Petti, et al 2019 scRNA mutation publicationmendelscan
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/sciclonerss2jira
Create JIRA issues when keywords are matched in RSS feeds.docker-rnaseq
A fat docker image for running RnaSeqUR
Rich Transactional Objects for Perlbmm
R package that uses a variational Bayesian approach to fitting a mixture of Beta distributionsdindel-tgi
A fork of dindeldocker-bcftools
Docker container for bcftoolsvcf-evaluation
scripts and modules to facilitate comparing gold standard VCFsdocker-bam_readcount_helper-cwl
graphite
Graphite Config and Cron Scriptsptero-lsf
Ptero services to run commands via LSFcle-chromoseq
Repository for CLE ChromoSeq Assaypairoscope
simple static plots of read pairing informationdocker-dna-alignment
A fat docker image for running alignmentaml31Benchmarking
cle-myeloseqhd
tgi-workflow
the workflow server used at TGIflow-core
cncwl
docker-vep-cwl
Variant of vep image without an ENTRYPOINTcle-myeloseq
Repo for cle myeloseq/haloplex assaydocker-gossamer
Docker container for gossamer bioinformatics suiteptero-workflow
Client-facing API for the PTero systemcle
Repo for cle related softwareqc-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 systemsomatic-snv-test-data
Example Data for SomaticSniperbuild-common
common build scripts used in c/c++ projectsnessy-client-perl
Perl client for the nessy-server lock daemonnessy-server
cancer-genomics-workflow-wiki
A full featured, including pull requests, git repo for the arvados_trial Wikidocker-fgbio
A docker image for using fgbiodocker-strelka
A docker image for StrelkaLove Open Source and this site? Check out how you can help us