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)
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.
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
Awesome! Thank you very much for your help