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Broad fungal method repository

License: BSD 3-Clause "New" or "Revised" License

WDL 96.23% Shell 1.11% Dockerfile 2.67%

wdl wdl-workflow firecloud fungal bioinformatics-pipeline snps

fungal-wdl's Introduction

Analysis pipelines for fungal genomic analysis

This repository contains workflows used by the Fungal Genomics group in the Infectious Disease and Microbiome Program (IDMP), the Broad Institute of MIT and Harvard.

Each directory in this repository corresponds to a workflow. Workflows are written in Workflow Description Language (WDL). Analysis environment was tracked using docker. Each workflow could be used on premise with the Cromwell Engine, or on the cloud with the Terra platform.

Workflow synopsis

gatk3: GATK3 fungal variant calling workflow
gatk4: GATK4 fungal variant calling workflow

About

This repo is developed and maintained by Fungal Genomics Group, IDMP, Broad Institute. Use issues tag to report any bugs.

This software is under BSD III license.

fungal-wdl's People

Contributors

Stargazers

Watchers

Forkers

faithgriffin wook2014 x-lab ovaibhav-m

fungal-wdl's Issues

Add BAM Alignment and QC module before alignment

add back scatter gather feature of GATK to speed up analysis

Current Analysis, Haplotype caller step is too slow.

write documentation for utilizing firecloud

For public release

Add variant QC modules

Variant Evaluation
Filter genotypes

get jars from online

currently in docker image, GATK and picard jars are directly copied from bin. Update the docker image such that those JARs are pulled from original online source.

update docker image to export tools to PATH

remove indel realignment

Terra tutorial

Given the Firecloud UI's retiring, update tutorial to Terra interface

docker image for the workflow

Downgrade from GATK4 to GATK3

GATK4 creates lower map quality scores.

add GATK filtering step

VCF genotype filtering

snpeff tests

fix output name from GVCF to VCF

Use compressed files in germline variant calling

fastq -> fq.gz
sam -> bam
vcf -> vcf.gz

Doc: Indicate GATK4 dockerhub links for ease of usage

Dockerhub links actually exist but were hidden from the documentation. Will need to add them back to the GATK4 documentation.

https://hub.docker.com/r/broadinstitute/fungal_gatk4
https://hub.docker.com/r/broadinstitute/python_fungal

Note that there's also personal copy from Aina's personal docker hub space. Just for the record.

https://hub.docker.com/r/amartine/fungal_gatk4
https://hub.docker.com/r/amartine/python_fungal

Environment and Runtime

use only one docker (one version of GATK)
update docker image to export tools to PATH
automate resource usage

Workflow improvement

Remove VQSR and BQSR
remove pre-emptible hard-coding
separate alignment from calling
fix output name from gvcf to vcf

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