taf-gatk

TAFFISH wrapper for GATK, the Genome Analysis Toolkit 4 from the Broad Institute.

This repository packages upstream GATK 4.6.2.0 as a TAFFISH tool app. It uses the official broadinstitute/gatk:4.6.2.0 Docker image as the runtime base and exposes the upstream gatk launcher through the versioned taf-gatk command.

Installation

Install from the public TAFFISH Hub index:

taf update
taf install gatk

Install the exact release:

taf install gatk 4.6.2.0-r2

For local testing before the app is published to the public index:

taf install --from .

Usage

Show TAFFISH app help:

taf-gatk --help

Show the TAFFISH package version:

taf-gatk --version

Show the upstream GATK version:

taf-gatk gatk --version
taf-gatk -- --version

List upstream GATK tools:

taf-gatk gatk --list
taf-gatk -- --list

Show help for an upstream GATK tool:

taf-gatk gatk HaplotypeCaller --help
taf-gatk gatk Mutect2 --help

Run a common germline variant-calling step:

taf-gatk gatk HaplotypeCaller \
  -R ref.fa \
  -I sample.bam \
  -O sample.g.vcf.gz \
  -ERC GVCF

Create a sequence dictionary:

taf-gatk gatk CreateSequenceDictionary -R ref.fa -O ref.dict

Index a VCF:

taf-gatk gatk IndexFeatureFile -I calls.vcf.gz

Pass JVM options to GATK:

taf-gatk gatk --java-options "-Xmx8g" HaplotypeCaller \
  -R ref.fa \
  -I sample.bam \
  -O sample.g.vcf.gz \
  -ERC GVCF

Run a local Spark tool:

taf-gatk gatk PrintReadsSpark \
  -I input.bam \
  -O output.bam \
  -- \
  --spark-runner LOCAL \
  --spark-master 'local[4]'

Because this is a command-mode TAFFISH tool, the first non-option argument is the in-container command. GATK tool names such as HaplotypeCaller, Mutect2, and GenotypeGVCFs are subcommands of the upstream gatk launcher, not standalone executables. The clearest and recommended form is therefore:

taf-gatk gatk HaplotypeCaller ...
taf-gatk gatk Mutect2 ...
taf-gatk gatk GenotypeGVCFs ...

The -- separator is useful for option-leading arguments sent to the default gatk command:

taf-gatk -- --help
taf-gatk -- --version
taf-gatk -- --list

The official image also exposes helper executables that Broad includes in the GATK Docker runtime:

taf-gatk samtools --version
taf-gatk bcftools --version
taf-gatk bedtools --version
taf-gatk tabix --help

For normal TAFFISH workflows, prefer the dedicated TAFFISH apps for those tools when they are separate workflow steps. They are kept inside this image because they are part of Broad's official GATK Docker runtime and are useful for GATK adjacent operations.

This README lists common usage patterns, not the full upstream manual. Use upstream help for the complete tool list and option surface:

taf-gatk gatk --list
taf-gatk gatk ToolName --help

Package

name: gatk
command: taf-gatk
version: 4.6.2.0-r2
kind: tool
image: ghcr.io/taffish/gatk:4.6.2.0-r2

Container

The container image is built from docker/Dockerfile using the official broadinstitute/gatk:4.6.2.0 image as the base.

This app intentionally keeps the official GATK runtime instead of rebuilding a minimal Java-only image. GATK 4.6.2.0 requires Java 17, uses Python for the gatk frontend and Python-based tools, and includes a Broad-maintained conda environment with Python and R packages used by selected GATK tools and plotting paths. The official image also includes samtools, bcftools, bedtools, and tabix.

Those bundled tools make the image large, but removing them would create a lighter image with a less faithful GATK command surface. A future gatk-lite or workflow-specific app could be useful for a narrow Java-only subset, but this gatk package is intended to track the official upstream Docker runtime.

The official upstream Docker tag is a single-architecture image. This TAFFISH release therefore declares native support for:

linux/amd64

For Docker and Podman, src/main.taf declares --platform linux/amd64, so Apple Silicon or other arm64 hosts may run this image through amd64 emulation without setting a global platform variable. That is a compatibility mode, not native arm64 support:

TAFFISH_CONTAINER_BACKEND=docker \
taf-gatk gatk --version

TAFFISH_CONTAINER_BACKEND=podman \
taf-gatk gatk --version

Apptainer behavior depends on the host and available architecture support.

The TAFFISH metadata declares a Docker smoke check:

exist: gatk, java, python, python3, R, Rscript, samtools, bcftools, bedtools, tabix
test:  gatk reports upstream version 4.6.2.0
test:  gatk --list includes representative tools such as HaplotypeCaller and Mutect2
test:  HaplotypeCaller help is available
test:  CreateSequenceDictionary works on a tiny reference FASTA
test:  IndexFeatureFile works on a tiny VCF
test:  PrintReads can round-trip a tiny synthetic BAM
test:  HaplotypeCaller can run on a tiny synthetic BAM and emit VCF

These smoke checks verify the container runtime and representative local GATK paths. They do not download reference bundles, validate Best Practices scientific output, run cloud authentication paths, or exercise external Spark, Dataproc, or large cohort workflows.

Each smoke command is self-contained because the public index runs every [smoke].test entry in a fresh temporary container. No smoke entry depends on files created by an earlier entry.

Upstream

• Source: https://github.com/broadinstitute/gatk
• Documentation: https://gatk.broadinstitute.org/
• Docker image: https://hub.docker.com/r/broadinstitute/gatk
• Release: https://github.com/broadinstitute/gatk/releases/tag/4.6.2.0
• Upstream license: Apache-2.0
• Citation: McKenna et al. 2010
• DOI: 10.1101/gr.107524.110
• PMID: 20644199