Questions tagged [allele-frequency]

Allele frequency is the foundational basis of the vast majority of population genetic calculations

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Population Allele Frequency

In UK biobank research environment In GENOMICS tab of UK BRAP, if I type 7:140476600-140480852 coordinate in search bar and the same time after filtering my cohort ...
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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 ...
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How to calculate Allele frequency from vcf file

Organism under investigation is Plasmodium falciparum. How to calculate the allele frequency for each row? I tried with this code: ...
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How to Recalculate Allele Frequency from a VCF File?

I have a VCF file with 200 samples (mitochondrial genome of Plasmodium falciparum). Here is a pic to take a look at: And a few relevant lines from the actual file: ...
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Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9

I downloaded the following vcf file from https://www.internationalgenome.org/. http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502....
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How can I fix "Ill-defined genetic structure" Error message in Arlequin?

I am performing an AMOVA analysis via Arlequin. At this point, I have: collected sequences of mtDNA from the cox1 gene, aligned the different genes using clustalX converted the files into .arp ...
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How can I use sequences with different lengths in arlequin?

I have mtDNA sequences of the cox1 gene from various populations of one species. I want to perform an AMOVA allele frequency analysis via Arlequin. This allele frequency package however requires my ...
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BAF and LRR calculation and usage

I'm working with a vcf file, in particular I'm trying to identify a gene duplication in a sequenced genome. I studied bcftools cnv command, but for this tool is needed a vcf file containing a BAF and ...
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What is the meaning of "Filtering allele frequency" in the gnomAD database?

Recent gnomAD versions include a "filtering allele frequency" which tells you when a variant can be safely adjudged not to be disease-causing. Unfortunately, I'm having trouble making sense ...
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Range of values for VAF in heterozygous genotype

(VAF = variant allele frequency) This question follows from this one. What is the expected range of values for VAF of mutations with heterozygous genotype (i.e., 0/1 or 0|1)? Is it possible to have 0% ...
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Assess ploidy estimation through SNV and CNV results

I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller. What are the ...
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Can an alternate allele be more common than a reference allele?

I'm trying to analyze data from a genotype-phenotype association study. The genotype data is stored in csv files that record for each variant site and each subject, the alleles that the subject has at ...
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Allele Count and Allele Frequency in VCF files

I'm working in bioinformatics, but my computational skills far outstrip my knowledge of biology or genomics. So forgive the noobish question. According to the VCF specification, the ...
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Populations genetics and dynamics of bacteria on a Graph

Disclaimer: I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense. My purpose: I would like to simulate genetic evolution of bacterial populations, ...
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Global SNP frequency database?

Is NCBI's dbSNP the most comprehensive database of SNP frequency? I'd like to get the largest possible database of allele frequencies per 'population' or geographic region. For example, on average, ...
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How can I find the position of every mutation where the Allele Frequency is greater than X, in regards to a reference such as Hg19?

I have a Human genome sequenced in a BAM file (along with other files with the indels, snps, cnvs). I want to find every mutation with regards to the reference Human genome. However the majority of "...
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creating population AF from set of individuals in 1000 genomes population?

What's the recommended way to create population-level Allele Frequency variant entries from a set of individuals (vcfs?) in the 1000 genomes (or similar) project? For example, given the IBS ...
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what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?

What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays? About 5 years or so ago, it used to be the latest release of the CSHL ...
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