AnswerBun.com

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

Bioinformatics Asked by a4xrbj1 on September 26, 2021

I want to add the frequencies of the genotypes to a baseline of raw DNA data I’ve got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all). All in build 37 human genome.

Where can I find that information? Checked HapMap project to no avail, can’t align with the rsId or positions used in the text files.

Thanks in advance for your help

2 Answers

gnomad is probably the most comprehensive allele frequency database that exists at the moment.

Depending on how many variants you need to query, you can either manually input them into the search bar, or if you have a lot more, then you can also directly download the vcfs under the downloads tab.

The default for V2 gnomad set is on the gr37 build.

Answered by user438383 on September 26, 2021

The largest number of samples is at the dbSNP database. To view frequencies of a single rsID in a web browser, for example, rs11950646, use the following URL:

https://www.ncbi.nlm.nih.gov/snp/rs11950646#frequency_tab

The dbSNP has more samples to calculate the frequency than gnomad, at least for this rsID.

If you need to automatically process multiple rsIDs, as you said, for the whole genotype file that you got from the companies like 23andMe, you can download a VCF with allele frequency data from https://ftp.ncbi.nih.gov/snp/population_frequency/latest_release/ and write a script to automatically process the data and make the output in a format you want. If you only need frequency of some rsIDs within a single chromosome, you can download the whole database for that chromosome from https://ftp.ncbi.nih.gov/snp/latest_release/JSON/ and will find the data in the JSON files, each file for each chromosome (plus the mtDNA). Look for the "frequency" field.

If you are not engaged to write scripts, and just wish to interactively browse various rsIDs in context of a frequency, you can upload your genotype file to selfdecode.com - it is a convenient, albeit a paid service.

Answered by Maxim Masiutin on September 26, 2021

Add your own answers!

Related Questions

NO_COOR reads not in a single block at the end 0 -1

1  Asked on May 19, 2021 by user9393

   

MUMmer plot error. Line 884. What to do?

0  Asked on May 18, 2021 by dansterboy

 

Is there public RESTful api for Gnomad?

5  Asked on May 14, 2021 by pasted

   

nextflow: Filter outputs of a process

1  Asked on May 10, 2021 by zillur-rahman

   

Filtering VEP annotation file

1  Asked on May 10, 2021 by jeni

   

Ask a Question

Get help from others!

© 2023 AnswerBun.com. All rights reserved. Sites we Love: PCI Database, MenuIva, UKBizDB, Menu Kuliner, Sharing RPP, SolveDir