GIABEval

Genome-in-a-bottle evaluation software to determine statistics such as precision, recall and f-measure.

Note that statistics calculations will be on the primary contigs as defined in nextflow.config. This prevents issues due to diffent reference genomes such als ALT, Decoy, or tertairy software reference genomes.

Get submodules, such as NextflowModules, CustomModules and install OpenJDK and Nextflow

sh install.sh

Usage

nextflow run main.nf -c nextflow.config --vcf_path [input_vcf_dir_path] --outdir [output_dir_path] --email [email]

Citations

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.