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B allele frequency (BAF)

Hi, I want to calculate B allele frequency from a vcf file. I found that vcftools can be used to estimate allele frequency of REF allele and ALT allele. I wonder if vcftools could also estimate B allele frequency. Are there other tools that we could use for calculation BAF from vcf file?

Thanks

snp
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updated by aidangcruickshank • aidangcruickshank • written by rthapa • rthapa

B allele frequency, like from a illumina genotyping array?

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written by curious curious

Not from Illumina genotyping array but from vcf file generated from NGS data.

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written by rthapa • rthapa

2 answers

There is a same question being answered:It seems that if you have a vcf file and AD in your GT field, it is an easy calculation. Calculate the b allele frequency from a VCF file .

A paper describing an R package that can do that : https://www.sciencedirect.com/science/article/pii/S1525157817301666

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written by s.guangchao • s.guangchao

If you are using R, you can take a look at the CopyNumberPlots Bioconductor package. Its focused on generating plots of BAF, LRR and copy-number segments from SNP-array and NGS, but it has a handy function to compute the BAF from a VCF where it will autodetect the presence of AD, GT and other formats for the allele depth. Just bear in mind that you need to set mirror.baf to false, since it will flip half of the allele frequencies to mimic the effect of the B-allele definition in Illumina arrays.

Using 

loadSNPDataFromVCF(vcf.file = "Your.vcf", genome="hg19", mirror.baf = FALSE)

you'll get a GRanges with the position and identifiers of your variants and their B-allele frequency ready to use.

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written by bernatgel bernatgel

Thanks a lot but the genome I am using is not the human genome.

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written by rthapa • rthapa

It should work with other genomes too. And I'm pretty sure it should be possible for it to work with unknown and custom genomes too.

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written by bernatgel bernatgel

Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documentation doesnt specify.

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written by aidangcruickshank • aidangcruickshank

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