I have recently obtained some relatively older genotyping dataset based on Illumina's Infinium Omni 5m platform for about 200 samples. In summary I have never analyzed this type of data before coming from a sequencing arena, I would greatly appreciate if someone can point me to relevant docs/ bioconductor packages.
here is what I am trying to do.
- analyze SNPs/genotypes across 200 odd samples
- filter out the low quality calls
- have a single file (may be a VCF) where SNPs are summarized for all the samples.
Many Thanks! -Abhi