ebdbcb/genomic_variant_call repository overview

Identify genomic variants using GATK.

A Genomic Variant Call refers to the process of identifying and characterizing genetic variations or variants within an individual's genome. These variants can include single nucleotide polymorphisms (SNPs), insertions, deletions, copy number variations, and structural variations. It uses GATK 4.2.6.1 (Genome Analysis Toolkit) to generate a GVCF (Genomic Variant Call Format) file from a BAM (Binary Alignment Map) file.

The current docker image is based on Ubuntu 22.04 and contains the following software:

• gatk 4.2.6.1 (https://github.com/broadinstitute/gatk/releases/download/4.2.6.1/gatk-4.2.6.1.zip⁠)
• miniconda (https://repo.anaconda.com/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh⁠)

It requires to mount the folder containing the scripts and data as a volume when running the docker image locally:

docker run -it -v /path_to_your_data:/data ebdbcb/genomic_variant_call /bin/bash

The Dockerfile used to build this image is available here: https://gitlab.com/ebd-bcb/dockerfiles/-/blob/master/dockerfile_genomic_variant_call⁠

More information at: https://gitlab.com/ebd-bcb/genomic-variant-call⁠

build by Raúl Ortega