How To Compare Snp Within Read Datasets?

Question

[alok.helix]

Dear freinds I have generated a .vcf files for 4 of my read dataset against my reference genome.Befor redirecting this file to the vcf-stats utility from vcftools, i utilized an indigenious perl script to seggregate snp's from indel which was present in the orginal vcf file. The vcf stats gave me individual stats for each read dataset and an overall count of snps in my file.

I want to compare snp's within the read datasets for the same .vcf file. I am considering two criteria's Base consensus Ratio and Read Depth. should i consider the BCR and DP for both or only one of the read set!! Is there any other criteria that i am missing out??

Thank u in advance!!

[Istvan Albert]

it is not clear what you want to achieve so it is difficult to answer your question. There is a genotype likelihood field that would tell you the probabilities, plus other scaled quantities that are better for comparison than say read depth.