gatk-workflows Goto Github PK

broad-prod-wgs-germline-snps-indels

Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline

five-dollar-genome-analysis-pipeline

Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline

gatk3-4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

gatk3-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK3 and related tools

gatk3-germline-snps-indels

Workflows for germline short variant discovery with GATK3

gatk4-basic-joint-genotyping

Basic joint genotyping with GATK4. NOT Best Practices, only for teaching/demo purposes.

gatk4-basic-variant-validation

Simple workflow to validate a VCF (or GVCF)

gatk4-cnn-variant-filter

This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

gatk4-genome-processing-pipeline

Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

gatk4-germline-cnvs

This repo will be archived soon, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

gatk4-jupyter-notebook-tutorials

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

gatk4-mitochondria-pipeline

This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-pathseq

This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

gatk4-somatic-cnvs

This repo is archived, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-somatic-snvs-indels

This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

gatk4-somatic-with-preprocessing

generic-wdl-script

This generic wdl script will be for users seeking to quickly run a shell command

intel-faster-alternative-samples

Miscellaneous workflows optimized by Intel to be fast-running

intel-gatk3-4-germline-snps-indels

Workflows for processing and variant discovery with GATK (v3+v4) optimized by Intel for on-premises infrastructure

intel-gatk3-germline-snps-indels

Workflows for processing and variant discovery with GATK optimized by Intel for on-premises infrastructure

intel-gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4 optimized by Intel for on-premises infrastructure

intel-gatk4-somatic-with-preprocessing

Workflows for data pre-processing and initial calling of somatic SNP, Indel, and copy number variants optimized by Intel for on-premises infrastructure

seq-format-conversion

Workflows for converting between sequence data formats

seq-format-validation

Workflows for validating sequence data formats

utility-wdls

Short workflows to run common tasks.