genomic-medicine-sweden/nallorefs

Introduction

genomic-medicine-sweden/nallorefs is a bioinformatics pipeline that downloads most of a set of references that genomic-medicine-sweden/nallo can use (but is not limited to).

For CADD-resources, CADD SNVs, GnomAD SNVs and dbNSFP, these files are so large that while the pipeline is able to download them, it might be better to download them manually. They can then be input into the pipeline with --cadd_annotations, --cadd_snvs, --dbnsfp and --gnomad_base_path (which should point to the directory where the gnomad chromosome VCFs are stored). The md5sum will be checked, and they will be processed by the pipeline.

These files can be downloaded with:

# Download CADD annotations
wget -c https://kircherlab.bihealth.org/download/CADD/v1.6/GRCh38/annotationsGRCh38_v1.6.tar.gz
# Download CADD SNVs
wget -c https://kircherlab.bihealth.org/download/CADD/v1.6/GRCh38/whole_genome_SNVs.tsv.gz
# Download gnomad
mkdir -p gnomad
cd gnomad
echo {1..22} X Y | tr ' ' '\n' | xargs -d ' ' -n 1 -P 10 -I {} wget -c https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr{}.vcf.bgz
# Download dbNSFP
wget https://usf.box.com/shared/static/2hzcx5s6p1xui7oen16xqzndfrkt8l9l -O dbNSFP4.5a.zip

Obtaining non-public reference files

The rank model downloaded with this pipeline also assumes you will input SpliceAI scores to VEP via --vep_plugin_files in Nallo. The precomputed spliceAI scores are available on basespace. Download the raw SNV and INDEL score files, rename them and place them in the reference directory.

SpliceAI/spliceai_scores.raw.indel.hg38.vcf.gz
SpliceAI/spliceai_scores.raw.indel.hg38.vcf.gz.tbi
SpliceAI/spliceai_scores.raw.snv.hg38.vcf.gz
SpliceAI/spliceai_scores.raw.snv.hg38.vcf.gz.tbi

Note

The rank models downloaded with this pipeline currently assumes you are using a local loqusdb database. To run without this, remove the [loqusdb] entries in the rank models.

Disclaimer

This software includes functionality to automatically download or reference publicly available datasets, files, or resources (“External References”) from third-party sources. These External References may be subject to their own license terms and conditions, including academic, research-only, or commercial restrictions.

The authors and maintainers of this software do not claim ownership or rights to any External References and do not redistribute them. The download functionality is provided solely for the user’s convenience, and it is the user’s responsibility to ensure that their use of any External References complies with all applicable license terms, institutional policies, and laws.

By enabling or using the download functionality, you acknowledge that:

• You are solely responsible for verifying and complying with the license terms of each downloaded dataset.
• The maintainers of this software are not liable for any misuse, infringement, or non-compliance with third-party license terms.
• You agree that this software is provided “as is” and without warranty of any kind, including but not limited to fitness for a particular purpose or legal compliance.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run genomic-medicine-sweden/nallorefs \
   -profile <docker/singularity/.../institute> \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

genomic-medicine-sweden/nallorefs was originally written by Felix Lenner.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

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.