Question: Variant frequency calculation
gravatar for nkausthu
2.8 years ago by
nkausthu20 wrote:

I have generated a multisample vcf file and also I have calculated each variant frequency across the samples using VCF tools as follows.

chr start end Ref Alt inhouseFreq

1 13418 13418 G A 0.231884

1 13494 13494 A G 0.00483092

1 13504 13504 G A 0.00241546

1 13525 13525 G T 0.00724638

1 13537 13537 C T 0.00966184

Along with frequency, I would also like to count homozygous and heterozygous states of each variant across the sample. Please give some suggestions regarding this.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by nkausthu20

One tool that might work is CRAVAT ( ). I believe it should show the zygosity of variants and frequency if you submit a VCF file.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Collin680

@ nkausthu, could you show which parameter of VCFtools that calculate variant frequency? What you have done is exactly what I wanted to do. Thanks!

ADD REPLYlink written 2.4 years ago by kin18210
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