Genetic measures calculation in vcf files

Question

[ricardo]

Hello.

I have a set of files in vcf format. They were obtained by mapping against a reference genome. After mapping the reads and identifying the SNPs, a selection of these was made based on a list of 40 genes. This was done for data from 18 different genomes. This way I have 18 vcf files, with the variations found in these genes of interest.

I would like to know what tools I could use to calculate some measures of genetic variability like pi, TajimaD and others. It is my interest to compare these values, since the data comes from various locations around the world.

I've tried using vcftools, but the results were not consistent, or I got error in the values (nan).

Answer 1

[willgilks]

Hi Ricardo,

I think you're getting values of NaN because you are only analysing one individual. Population genetics requires more than one individual, of course.

Combine the separate vcf files from each individual into one, then analyse.

GATK is good for this function http://gatkforums.broadinstitute.org/gatk/discussion/53/combining-variants-from-different-files-into-one