Difference between a VCF file and a "genotype matrix" ?

Question

[stevenlang123]

I'm using NGS data to run a program that asks for a "genotype matrix" of samples and SNPs. Is this just the same as a VCF file?

Answer 1

[Jeremy Leipzig]

Usually it is a representation of the sample GT calls in the VCF file that represents alleles at that position (i.e. 0: homozygous ref, 1: heterozygous alt, 2: homozygous alt)

snp                       sample1     sample2     sample3
1:2348932A>C                    0           1           2

VCF is the right starting point. In R:

library("VariantAnnotation")
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
mat <- genotypeToSnpMatrix(vcf)
t(as(mat$genotype, "character"))

[stevenlang123]

I see. Do you know of any tools that can create such a file from a set of .BAMs? The exact specification for the file I need to create is the following: 1st column: gene name; 2nd column: snp name; 3rd-end columns: A matrix of genotypes for each subject (class: data.frame). The order of 3rd-end columns should match id. Coded as 0, 1, 2 and no missing.

Thanks in advance

[stevenlang123]

Awesome! Thank you very much for your help