Tools to work with variant call format files

Bayesian haplotype-based mutation calling

A configurable generator of simulated RNA-Seq data that can emulate any specific biological mechanism and provide robust data sets covering cases such as fusion genes (or fusions).

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

CWL pipelines for the Sentieon tools

Scalable mpi aligner base on BWA

cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.

generate germline and somatic variants in VCF format

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

Python package to extend Airflow functionality with CWL1.1 support

Framework for testing CWL tools and workflows

Structural variant and indel caller for mapped sequencing data

SNAP-IT: Spliced Neoantigen Pipeline for Immunotherapy

CNV Rapid Aberration Detection And Reporting

Thousand Variant Callers Project Repository

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

CWL tools and workflows for GGR

Fast and accurate gene fusion detection from RNA-Seq data

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Dockstore implementation of bamtofastq (biobambam2)

Command-line tool to soft-clip reads based on primer locations.

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Import and run CWL workflows on DNAnexus (alpha)

Strelka2 germline and somatic small variant caller

Tools to help users with navigating arvados on the command line

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

Import a CWL workflow specification to Nextflow script (experimental)