comparing two illumina genotypes report

Question

[tarek.mohamed]

Hi All,

I have two final illumina reports from bead chip experiment (300,000 SNPs). Ideally genotypes of these two samples should be identical. How can I compare between the genotypes of the two samples to see if they are really identical or there are some mismatches?

The files look like this;

CHROM   POS             ID              Sample_ID           Allele1  Allele2   GC_Score

3       183635768       rs1000002       200638550003_R01C01     A       G       0.8902

3       98342907        rs1000003       200638550003_R01C01     A       G       0.9351

4       103374154       rs10000030      200638550003_R01C01     A       G       0.7764

4       38924330        rs10000037      200638550003_R01C01     G       G       0.929

4       165621955       rs10000041      200638550003_R01C01     A       A       0.8957

2       237752054       rs1000007       200638550003_R01C01     A       G       0.9491

Thanks Tarek

Answer 1

[Zev.Kronenberg]

How about converting the files to VCF then using one of many VCF comparison tools?

[tarek.mohamed]

Hi Kronenberg, Thanks for the reply! What would be the best way to convert illumina genotype report to VCF?

Regards Tarek