CAAD score for SNPs vcf file

Question

[Eliza]

Hi, I have a VCF file of only SNPs. what I wish to do is for every SNP to download the CADD score from here: https://cadd.gs.washington.edu/download
. I'm new to genetics and I'm not sure which file should i download for this :

is it the Genome build GRCh37 / hg19-All possible SNVs of GRCh37/hg19 or All possible SNVs of GRCh38/hg38 or the All gnomAD SNVs (release 2.1.1)? I'm suspecting that I should download All possible SNVs of GRCh38/hg38 (but it is a very big-81G, if this is the file would appreciate to know what is the code to download it in UBUNTU is this the same as downloading gnomad data?)

This is what my VCF file to which I would like to add the CAAD scores looks like :

Answer 1

[barslmn]

Whether you need to download hg19 or hg38 depends on the assembly of your data. If you have a small amount of variants you can just use their web app https://cadd.gs.washington.edu/score or ensembl VEP web.

Also, above your screenshot there is a link with the text “README” which goes to their GitHub. https://github.com/kircherlab/CADD-scripts/ Where you can find instructions on how to install and how to use.

[Eliza]

Thank you . Just to make sure if I'm working with SNPS is this file the correct one All possible SNVs or should I use the gnomad option there ?

[barslmn]

gnomAD and CADD are different resources.

from CADD website

CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

from gnomAD website

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.

I suggest you go to their sites and click around a bit to see what they are about.