VCF file with AF(allele frequency)

Question

[Parimala Devi]

Hi,

I need to analyse SNPs based on Allele frequency(AF) and not the AF1. The vcf file I obtained by using samtools excludes the INFO for AC.

##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  A.sorted.bam
Y55.chr10       5       .       N       C       24.0    .       DP=15;VDB=8.264144e-07;AF1=1;AC1=2;DP4=0,0,15,0;MQ=12;FQ=-72    GT:PL:GQ        1/1:57,45,0:66
Y55.chr10       6       .       N       C       23.0    .       DP=16;VDB=6.101920e-07;AF1=1;AC1=2;DP4=0,0,16,0;MQ=11;FQ=-75    GT:PL:GQ        1/1:56,48,0:68
Y55.chr10       7       .       N       A       22.0    .       DP=16;VDB=6.101920e-07;AF1=1;AC1=2;DP4=0,0,16,0;MQ=11;FQ=-72    GT:PL:GQ        1/1:55,45,0:64

Is there any way I can obtain the allele frequency in my vcf? Any other variant calling tool that would provide me with the AF?

Thank you,
Parimala

[Anop Singh Ranawat]

Estimating AF from DP4 in a VCF file

you should go http://gatoravi.github.io/work/2016/05/07/mpileup_AF.html

Answer 1

[gsr9999]

bcftools plugins can be used to get the AF tag and value to your vcf file

export BCFTOOLS_PLUGINS="~/bcftools/bcftools-1.3.1/plugins/"
bcftools plugin fill-tags -Oz -o output_variants.vcf -- -t AF

Answer 2

[Naga]

If you are looking for frequency of variants in the population, i.e., Minor allele frequency (MAF), annotate the variants with 1000 genome data or ExAC.

And if you are looking for variant allele frequency (VAF), to determine, whether it is heterozygous or homozygous, use DP4 field.

DP4 is Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling.

VAF = (forward non-ref + reverse non-ref alleles) / (forward ref alleles + reverse ref + forward non-ref + reverse non-ref alleles)

[Parimala Devi]

Thank you for the reply. I'm looking for the Allele frequency AF in the INFO. I have 2 vcf files. I need to plot a graph comparing the AF at each position for each chromosome using the 2 vcf files. I used the following command from vcftools.

./vcftools --vcf input_data.vcf --freq --out output

CHROM POS N_ALLELES N_CHR {ALLELE:FREQ}
Y55.chr10 5 2 2 N:0 C:1
Y55.chr10 6 2 2 N:0 C:1
Y55.chr10 7 2 2 N:0 A:1
Y55.chr10 8 2 2 N:0 C:1
Y55.chr10 9 2 2 N:0 A:1
Y55.chr10 10 2 2 N:0 C:1
Y55.chr10 11 3 2 N:0 C:1 A:0

Could anyone explain the columns?

Thank you,
Parimala