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GATK3 variant calling workflow

This repository contains GATK3 based variant calling pipelines used by the Fungal Genomics group in the Infectious Disease and Microbiome Program, the Broad Institute of MIT and Harvard.

The pipeline input is set of unaligned (or aligned) BAM files and a reference genome. Reads are converted to FASTQ and aligned with BWA, alignments sorted and marked for duplicates with Picard, SNPs joint-called using GATK HaplotypeCaller, and hard filtration using GATK variant filtration. The output is a multi-sample VCF file.

Synopsis

  • README.md: this file
  • docs: documentations and tutorials
  • tests: files used for testing the workflow
  • workflows: variant calling workflow. Note that fungal_variant_calling_gatk3.wdl is the full WDL, while haplotype_caller_scatter_gatk3.wdl is a module that the former uses.
  • Dockerfile: docker image for the workflow. The docker is also available from dockerhub here.

This method was deployed on Terra Method Repository here. Example Terra workspace can be found here.

A tutorial to customize the workspace and import your data could be found here.

Software versions

PICARD_VER=1.782
GATK37_VER=3.7-93-ge9d8068
SAMTOOLS_VER=1.3.1
BWA_VER=0.7.12
TABIX_VER=0.2.5_r1005
BGZIP_VER=1.3

About

This repo is developed by Xiao Li from IDMP, the Broad Institute. Use issues tag to report any bugs.