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
1 answer
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
it has different data
no, there is one line for each ALT allele at the very same position (normalized VCF)
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