4
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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 .
3
votes
Accepted
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__♦
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2
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 ...
- 3,141
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 ...
- 1,105
2
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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 ...
- 241
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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....
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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 ...
- 141
1
vote
Accepted
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 ...
- 3,804
1
vote
Accepted
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" ...
- 827
1
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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 ...
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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, ...
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