WGS nf-core raredisease test

This project aims on testing the nf-core raredisease pipeline for usage with whole-genome sequencing short-read Illumina data.

Data

For testing we use the GIAB Ashkenazim trio patient samples:

Son: HG002 Father: HG003 Mother: HG004

These were sequenced using Illumina WGS 2x 250bp technology, more information about library prepration and sequencing can be found in the README.

Data was downloaded from NCBI FTP server and indexes extracted from https://github.com/genome-in-a-bottle/giab_data_indexes on 8th August 2023.

Workflow

1. Download workflow and singularity images

nf-core download raredisease --revision 1.1.1 --compress none --container-system singularity --container-cache-utilisation copy

2. Download and adapt references and plugins

This workflow requires the nextflow plugins nf-validation and nf-amazon. For offline deployment, follow this hint.

• nf-validation v0.3.1
• nf-amazon v1.16.2

References:

The list of references needed is explained in the usage and params documentation: https://nf-co.re/raredisease/1.1.1/docs/usage & https://nf-co.re/raredisease/1.1.1/parameters

• Reference genome GRCh38
  • downloaded from GIAB
  • wget --recursive -e robots=off --reject "index.html" --no-host-directories --cut-dirs=6 https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/ -P $PWD
• VEP cache version 107
• strangers variant catalog file for --variant_catalog
  • from: https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json
  • According to new usage documentation in dev branch (nf-core/raredisease#380)
• gnomAD
  • downlaod from official website https://gnomad.broadinstitute.org/downloads#v3
  • reformatting with vembrane table vembrane table --header 'CHROM, POS, REF, ALT, AF' 'CHROM, POS, REF, ALT, INFO["AF"]'
  • Add comma between REF adn ALT with awk.
  • WARNING: only used chr1 for testing the first run
• CADD resources: https://cadd.gs.washington.edu/download "All possible SNVs of GRCh38/hg38" and data/annotations folder
  • for cadd_resources parameter to annotate indels: "Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described here, and it is used to calculate CADD scores for small indels.": annotationGRCh38_v1.6.tar.gz
• from the official test datasets ():
  • vcfanno config (toml) and adapted resources
  • svdb
  • score_config_snv: https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini
  • score_config_sv: https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_sv.ini

3. Run

For first run, limited analysis as following:

• gnomAD only with chr1 (due to slow download)
• skip CNV calling (missing ploidy and gcnvcaller model)

Citation

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