GATK-Allele frequency

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?

vcf allele gatk frequency

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updated 3.7 years ago by johnston.mike.j •

• written 4.8 years ago by shivangi.agarwal800

The information you provide is insufficient to get the right answer

is your VCF file multi-sample?

your variants are biallelic?

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written 4.8 years ago by reza

1 answer

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.

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written 4.8 years ago by Pierre Lindenbaum

Yes, there is only one sample.

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written 4.8 years ago by 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

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written 4.8 years ago by shivangi.agarwal800

Calculation of VAF (variant allele frequency)

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

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written 4.8 years ago by Pierre Lindenbaum

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

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written 4.8 years ago by shivangi.agarwal800

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

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written 4.8 years ago by Pierre Lindenbaum

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

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written 4.8 years ago by shivangi.agarwal800

I already answered.

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written 4.8 years ago by Pierre Lindenbaum

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?

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written 4.8 years ago by shivangi.agarwal800

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)

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written 3.7 years ago by johnston.mike.j •