Variant frequency calculation

Question

[nkausthu]

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.

[Collin]

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

[kin182]

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