SNPs density ( count/ per Kb) calculation from VCF file

Question

[BioRyder]

Hello All,

I want to calculate SNPs/KB density count from a Quality filtered (GATK hard filter and Individual Filter) VCF file. Below are the steps I have performed for calculating SNPs per Kb density.Total samples are 188.

1. vcftools --vcf input.vcf --SNPdensity 1000 --out SNPs_densityPerKb
2. Count the 1kb bins from SNPs_densityPerKb ( 848770 )
3. Total Number of SNPs : 7075927
4. SNPs /Kb = 7075927/848770 ( total SNPs/ total 1kb bins)

I just want to confirm my SNPs /Kb calculation is right or Not.

Please somebody can comment it.

Answer 1

[mgalland1983]

Hello BioRyder, Reading the VCFtools documentation:

--SNPdensity <integer> Calculates the number and density of SNPs in bins of size defined by this option. The resulting output file has the suffix ".snpden".

As far as I understand it, vcftools will already calculate the SNP density per 1000nt window (1kb window) so you do not need to calculate anything any further. Already done!