Minor Allele Frequency calculation from VCF file

Question

[a.james]

Hello All

I am using GATK RNA-seq variant pipeline for finding mutation/variant calling on the list of gene given in the following command line

java-1.7 -jar -Xincgc -Xmx1586M GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller --filter_reads_with_N_cigar -R human_genome37_gatk.fa -D dbsnp_137.hg19.vcf -I sample_split.bam -o sample.vcf -L mylist.intervals

And the resulting VCF files has for variants AF either 100 % or 50 % . It would be great if anyone would explain me what does AF means in INFO column from VCF file. example,

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    sample
chr1    564598    rs6594028    A    G    15123.77    .    AC=2;AF=1.00;AN=2;DB;DP=392;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.09    GT:AD:DP:GQ:PL    1/1:0,389:389:99:15152,1167,0
chr1    564654    rs147404388    G    A    15595.77    .    AC=2;AF=1.00;AN=2;DB;DP=422;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.40    GT:AD:DP:GQ:PL    1/1:0,419:419:99:15624,1255,0
chr1    564862    rs1988726    T    C    476.77    .    AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.66    GT:AD:DP:GQ:PL    1/1:0,11:11:36:505,36,0

It would be great if someone could share how to calculate Allele frequency from the VCF file..

[lh3]

See VCF spec. AF is the alternate allele frequency.

[a.james]

The AF field from the VCF file is the theoretical allele frequency that corresponds to the genotype call made by the tool.

Answer 1

[EagleEye]

http://samtools.github.io/hts-specs/VCFv4.1.pdf http://samtools.github.io/hts-specs/VCFv4.2.pdf