Extracting SNPs that differ in genotype between two individuals.

Question

[pharmaviator]

Hi,

I used genome studio to generate data for married couples, HumanCore-Exome Chip was used.

is there a way to extract only those SNPs that have different genotypes between each husband & wife? is there a way to extract genes for them if the first step of extracting SNPs is feasible?

Thanks

[GenoMax]

How to compare 2 VCF files
Compare Vcf Files

[pharmaviator]

I want to compare the calls like for example if his SNP is A and hers is C for example and end up only with SNPs that have different calls. My files are in the following formats: TXT, PED, BED, XLSX.

I have 23 couples, can I still do it ?

Answer 1

[Sean Davis]

Yes, but you will probably need to do that using R, python, or some other language. It could be done in Excel, I suspect, but I wouldn't recommend that approach.

[pharmaviator]

Excel is not capable of handling big data sets ... when the number of cells is huge it crashes.