I'm reading an interesting paper, [Malachi et al., Cell Systems 2015][1], that talks about Variant Allele Frequency (VAF). Could someone please help me understand how they calculated this value? I couldn't find it in the methods.

**edit**

For example, let's say I have a bunch of VCF files that I would like to find VAF for. How would I go about doing that? Here's an example of a VCF file:

    ##fileformat=VCFv4.1
    ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
    ##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance of Alt Allele">
    ##INFO=<ID=RD,Number=1,Type=Integer,Description="Depth of Ref allele">
    ##INFO=<ID=AD,Number=1,Type=Integer,Description="Depth of Alt allele">
    ##INFO=<ID=SAP,Number=1,Type=Float,Description="Strand Bias Probability of the Alt Allele">
    ##INFO=<ID=RAP,Number=1,Type=Float,Description="Strand Bias Probability of the Ref Allele">
    ##INFO=<ID=DP4,Number=4,Type=Float,Description="Fwd Strand Ref Counter, Rev Strand Ref Counter, Fwd Strand Alt Counter, Rev Strand Alt Counter">
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
    ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
    #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	genotype
    chr1	808922	.	G	A	249	PASS	DP=49;AB=1.0000;RD=0;AD=49;SAP=0.5510;RAP=0;DP4=0,0,27,22	GT:GQ:DP	1/1:145:49
    chr1	808928	.	C	T	249	PASS	DP=51;AB=1.0000;RD=0;AD=51;SAP=0.5294;RAP=0;DP4=0,0,27,24	GT:GQ:DP	1/1:145:51
    chr1	876499	.	A	G	217	PASS	DP=49;AB=1.0000;RD=0;AD=49;SAP=0.6939;RAP=0;DP4=0,0,34,15	GT:GQ:DP	1/1:126:49




  [1]: http://www.cell.com/cell-systems/fulltext/S2405-4712(15)00113-1
Variant allele frequency in this case refers to the fraction of sequencing reads overlapping a genomic coordinate that support the non-reference (mutant/alternate) allele.

Typically, this information is either explicitly listed or readily extractable from VCF files. If not, given that you have the genomic coordinates of the mutation of interest and the bam file, you can run [samtools mpileup][1] command to get the alleles coming from the entire set of overlapping reads.

I use a [python script][2] to parse the output of mpileup into a human-readable allelic table.

  [1]: http://samtools.sourceforge.net/mpileup.shtml
  [2]: https://github.com/Niknafs/NGSTools/blob/master/baseParser.py