GATK Variant calling pipeline for genomic data using Nextflow
Install Nextflow using the following command:
curl -s https://get.nextflow.io | bash
Index reference genome:
$ bwa index /path/to/reference/genome.fa
$ samtools faidx /path/to/reference/genome.fa
$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict
Launch the pipeline execution with ...
Submitter: Jeffrey Detras
Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...
Type: Shell Script
Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun
Submitter: Georgina Samaha