matching gnomAD allele frequency
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11 months ago
sooni ▴ 20

Is there a way to find the allele frequency of gnomAD db with the rsID of my SNP data using gnomAD db in Python or R?

If there is a specific rsID, I want to get the total allele frequency and east asian allele frequency of this rsID from gnomAD db.

I tried using the gnomAD_DB package in python, but there were many cases where the allele frequency could not be obtained. I think this part is strange, so I'm looking for another way.

Please help me.

R python gnomAD • 1.1k views
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11 months ago
raphael.B ▴ 520

It's not python or R, but vcfanno allows to do this quite simply and fast

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11 months ago
bk11 ★ 2.8k

Since you want to check for a specific SNP, why don’t you look in dbSNP? You ll find allele frequency of your SNP of interest in different databases and a wide range of populations.

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I am trying to download dbSNP data from NCBI. Is it right to download via FTP? There are several types of files. Which file should I download to get allele frequency information?

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11 months ago
luffy ▴ 130

sooni why not annotate your variants with ensembl vep, you either use their web version or install locally if the number of variants are large. You can choose to select to annotate only gnomAD or with any other data as well. Hope this helps

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