Allele Frequency Calculator

The Allele Frequency Calculator

VCF files of variant sites and genotypes, released by the 1000 Genomes Project, are usually annotated with allele frequencies (AF) at the global and continental super population levels. Many users also want the AF of certain variants for the specific populations of interest. The AF Calculator provides an interface to generate AF for variants in a given genomic interval for a given population. If no specific population is specified, the tool will calculate and output AF for every population in the input files.

Input Files:

The AF Calculator takes a VCF file containing individual genotypes and a sample to population mapping file as input files. Both these files are released by the 1000 Genomes Project as part of their standard released on the project FTP site. The tool will also work with external files independent from the project, provided they are publicly visible. Local files can be used as input to the API Perl script of the Calculator.

The VCF file format specifications can be found at the hts-specs website.

The VCF files must be indexed by tabix. All vcf files found on the 1000 Genomes FTP site are indexed using this method. The tabix software is available from the SAMtools sourceforge project.

The sample to population mapping file is a tab-delimitated file; the first column is sample id; the second column is population. Additional columns will be ignored. An example can be found at the project ftp site in the phase1 integrated variant calls directory:

https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/integrated_call_samples.20101123.ALL.panel

The calculator must be given a genomic interval to define which sites are to have their frequencies calculated. For the web-based tool we recommend an interval shorter than 5 Mbases to ensure the tool returns in a reasonable time frame.

After you click the “Next” button, you may choose a population from a dropdown menu. If you choose “ALL” as population, the AF will be calculated for every population in the VCF file.

Output:

The output of the calculator can be previewed on the web page and an output file can be downloaded.

Here are a few lines from an example of output file:

POS	ID	REF	ALT	TOTAL_CNT	ALT_CNT	FRQ
22	17004085	rs182269758	A G	170	9	0.05
22	17004141	rs192917218	A G	170	2	0.01
22	17004902	rs4010207	A G	170	12	0.07
22	17004113	rs186630910	A G	170	9	0.05
22	17004057	rs187809646	A G	170	11	0.06
22	17003679	rs2890298	A G	170	12	0.07
22	17004914	rs5992906	C T	170	66	0.39
22	17004058	rs190038164	T C	170	4	0.02
22	17004861	rs4010206	C T	170	0	0
22	17004497	rs142081770	G T	170	0	0
22	17004071	rs9605433	G A	170	17	0.1
22	17004153	rs9680545	G A	170	16	0.09
22	17004454	rs8135289	T C	170	71	0.42
22	17004348	rs28417007	T A	170	0	0
22	17003990	rs146134165	A C	170	28	0.16
22	17003695	rs56873984	C T	170	17	0.1
22	17004593	rs145217318	T A	170	0	0
22	17003703	rs191454176	G A	170	0	0
22	17003987	rs184186321	T A	170	11	0.06

The header is:

CHR: Chromosome
POS: Start position of the variant
ID: Identification of the variant
REF: Reference allele
ALT: Alternative allele
TOTAL_CNT: Total number of alleles in samples of the chosen population(s)
ALT_CNT: Number of alternative alleles observed in samples of the chosen populations(s)
FRQ: Ratio of ALT_CNT to TOTAL_CNT