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Questions tagged [gnomad]

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Variant allele frequency versus population frequency

In gnomAD related article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9160216/#:~:text=Allele%20frequency%20is%20calculated%20by,can%20differ%20substantially%20between%20positions I road this section ...
Zizogolu's user avatar
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2 votes
1 answer
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Availability of information on genes in Gnomad VCF data

I was wondering does the gnomad genome data that is downloaded in the vcf format on variants contain information on what is the nearest gene and is the genomic location available exome/intron? if yes ...
agnesa rivkin's user avatar
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1 answer
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SNPs location out side the gene

I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
Eliza Romanski's user avatar
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1 answer
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Allele frequency gnomad data

I noticed that some gnomad SNPs have allele frequency =0 and some are just not found : No genes were found in this region. what is the difference between them : for example:Y-10010520-10010520. Is all ...
Eliza Romanski's user avatar
1 vote
1 answer
114 views

Is picking variants belonging to a specific group of genomes from VCF file possible?

GnomAD has publicly available VCF files that have variant data gathered from over 15k individuals. For a university project, I want to randomly select 1k of these individuals and get the variant data ...
Arda Cüce's user avatar