gnomad data for chrx

Question

[Eliza]

Hi,

I'm new to gnomad and genetics. I downloaded data from gnomad of chrx:

I filtered the data to have only SNPs. What I wanted to extract from the data is for each SNP I would like to get the allele freq - AF in INFO column and AF_amr - allele freq of Latin population. What I don't understand is this situation that the same dbsnp in the same position has different data for those attributes, maybe I'm not looking at the data correctly.

What I wish to do with this is: I have SNP data on which I performed some statistical calculations it look like this:

The data is much longer. What I want is for every SNP in my data to join allele freq from the gnomad data. So I don't understand how can I take the data from gnomad and join it if for example for chrx-67943482 it has different data?

Thank you

Answer 1

[Pierre Lindenbaum]

if i understand correctly ID is the ID of a person t

it's not, it's an identifer in a database, here dbsnp . After your previous question (Gnomad vcf data info column ) I strongly suggest your read the VCF specification. https://samtools.github.io/hts-specs/VCFv4.2.pdf

[Eliza]

@Pierre Lindenbaum, thank you read it but would really be happy to get some help after I edited the Q as I don't understand how to work with the GNOMAD data

[Pierre Lindenbaum]

it has different data

no, there is one line for each ALT allele at the very same position (normalized VCF)

[Eliza]

@ Pierre Lindenbaum if I understand you correctly if I want to join it with my data then in my data I should check what is the ALT and REF at a specific position and join based on that?