Hi, I have a sample ran with Illumina SNParray and WES, and I need to compare their data.
What is the best method to compare them?
I was trying using the VCF:
From WES data I created a VCF, but from SNParray data seems a little tricky to have the vcf ...
GenomeStudio gives as output a plink format, and then I can convert it to VCF using plink. Reading around, seems that I have to check if the Reference Allele in the VCF is correct ... I checked it using GATK validate VCF and in some cases the reference allele is not correct. The fact that is not correct, is it due only because it is the complement base (I see plink2 has the option --flip) or could be the case that in the SNParray manifest could be Ref and Alt inverted? Seems that for the manifest is not important if the Alt allele is in the Ref position ...
Thanks
