GATK-Allele frequency

Question

[shivangi.agarwal800]

Hi Guys,

I am running GATK on bam file for variant calling. In the output file, I noticed that the Allele frequency is computed as 0.5 and 1.00. What may be the reason for this? Is it calculated correctly?

[reza]

The information you provide is insufficient to get the right answer

is your VCF file multi-sample?

your variants are biallelic?

Answer 1

[Pierre Lindenbaum]

do you have only one sample ? the genotype is either heterozygous AN=2 AC=1 then AF=0.5 , or homozygous on ALT allele: AN=2, AC=2 then AF=1.0.

[johnston.mike.j]

If you are looking to add VAF values, consider using:

bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t FORMAT/VAF

See bcftools plugin docs here:

https://samtools.github.io/bcftools/howtos/plugin.fill-tags.html

And further discussion of MAF and VAF here:

Calculation of VAF (variant allele frequency)

[shivangi.agarwal800]

Yes, there is only one sample.

[shivangi.agarwal800]

Hi,

How this allele frequency is calculated? I did not get it. Can you just brief me and send me a link to read about it. ?

Thanks

[Pierre Lindenbaum]

Calculation of VAF (variant allele frequency)

freq(a) =( sum(samples_with_geno_aa x 2) + sum(samples_with_geno_Aa)) / (samples x 2)

[shivangi.agarwal800]

Hi,

Thank you so much. I want to confirm whether Allele frequencies were calculated correctly for one sample. Also, If I have more than one samples, how to proceed for variant calling. I mean we have to calculate separately for each sample ??

Thanks

[Pierre Lindenbaum]

https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode

[shivangi.agarwal800]

Hi Pierre,

I am new to this analysis. Can you please guide me how AF is coming as 0.500 and 1.000? I will really appreciate your support.

Thanks

[Pierre Lindenbaum]

I already answered.

[shivangi.agarwal800]

Hi Pierre,

Thank you so much. The link you provided is very helpful which includes two aspects as Joint Variant Calling (from bam) and Joint Genotyping (from vcf). I found command for Joint genotyping https://biohpc.cornell.edu/lab/doc/Variant_exercise.pdf.

However, I could not find any command for variant calling from multiple bam files. Can you please help in this regard?