IRRI Bioinformatics Group
OverviewSpace: IRRI-Bioinformatics
SEEK ID: https://workflowhub.eu/projects/149
Public web page: Not specified
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Team created: 21st Mar 2023
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https://orcid.org/0000-0002-6680-578X
SNP-Calling
GATK Variant calling pipeline for genomic data using Nextflow
Quickstart
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 ...
