Ok I a fairly new to both SNV calling and chip arrays. Most of my experience is with RNA-seq, alternative splicing etc.
Now, I have some data from Illumina's Human CytoSNP12 bead array that I want to analyze. I used GenomeStudio and I got all the tables, and most of what I see makes sense. My only issue is that, if you analyze cancer patient's samples and you try to find rare SNPs in their samples, what is the confidence that let's say BAF of 1% is actually true and not background or other weird things that may interfere with the technology and software?
Is there a minimum BAF percentage that we can use with confidence? 5%? 10%? I know that in NGS depending on the depth of sequencing and if you use molecular barcodes to distinguish true copies vs PCR duplicates you can go to 5% and call it with confidence.
Any body knows what people have been using for Illumina's arrays and GenomeStudio software? I'm getting some SNVs in the 1-5% BAF but I don't know if I should use them or not.