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4 votes

what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?

The best set I'm aware of can be downloaded from https://gnomad.broadinstitute.org .
Christopher Chang's user avatar
3 votes
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Allele Count and Allele Frequency in VCF files

No, that is not quite right. specifically, this part: And by "hit" I mean an aligned sequence fragment that includes that coordinate. To get data on how many reads contributed to calling a ...
conchoecia's user avatar
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3 votes
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Populations genetics and dynamics of bacteria on a Graph

I assume you are simulating a null distribution. Are you investigation recombination?? My main advice is to use population genetic terminology rather than geomometry to describe your simulation (e.g. ...
M__'s user avatar
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3 votes
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Population Allele Frequency

I don't know specifically about the UKBB RAP, however, Population Allele Count is the count of that specific allele genotyped in the population in question. In this case, it most likely refers to the ...
Yossi Farjoun's user avatar
3 votes
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Variant allele frequency versus population frequency

gnomAD provides a global Allele Frequency as well as AF values for most subsets. gnomAD does not provide individual genotypes (as far as I know), so calculating custom AF for non-precomputed subsets ...
Ram RS's user avatar
  • 2,310
2 votes

How to Recalculate Allele Frequency from a VCF File?

It sounds like your main confusion is how to calculate AF. I'll answer that right away, but I'll also suggest a Python library that you can use to do this and much more. You're correct, the AF is ...
Daniel King's user avatar
2 votes

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?

Hello and welcome to the world of bioinformatics, BAM files are compressed formats of SAM and you can read more about it here. To answer your question, I presume that your BAM is generated from a ...
user324810's user avatar
  • 1,115
1 vote
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creating population AF from set of individuals in 1000 genomes population?

bcftools has a plugin called fill-tags which should do the job for you easily, without having to mess around with lots of complicated bash scripting. You could do something along the lines of this, ...
user438383's user avatar
  • 1,679
1 vote

Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9

The standard and most common way to name SNPs is by using rsIDs. The reason your output from PLINK does not include SNP names is because these are not included in the original VCF you are working with....
JRodrigoF's user avatar
  • 827
1 vote

What is the meaning of "Filtering allele frequency" in the gnomAD database?

My understanding is from Whiffin et al. 2017. Imagine a dominant mendelian disease A with complete penetrance, caused only by one allele, which is currently unknown. In your search for that unknown ...
ning's user avatar
  • 141
1 vote
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Range of values for VAF in heterozygous genotype

From the link that I edited into your question (realized that the answer was there): VAF is the percentage of sequence reads observed matching a specific DNA variant divided by the overall coverage ...
Maximilian Press's user avatar
1 vote
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Can an alternate allele be more common than a reference allele?

You are mixing up a bit the terminology here. One thing is a reference allele and another is a major allele. The first refers to the genotype present at a given position in the "reference" ...
JRodrigoF's user avatar
  • 827
1 vote

Can an alternate allele be more common than a reference allele?

Yes, depending on how the reference allele was determined. If, for example, you want to refer to hg38 as the reference genome, then it's important to use the hg38 allele as reference. Without stating ...
gringer's user avatar
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