Test-drive the GATK tools and Best Practices pipelines on Terra
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VQSR with two data sets
I would like to Build the SNP recalibration model with two data sets.
1- SNPs derived from WGS and filtered
2- SNps derived from SNP array chip data
The problem that I have is that the SNPs from the chip data do not have any information such as coverage or any other information. They just have the genotyope and the position. Of course I could convert this data to a vcf but without any more info. It is still possible to use this data to run the VQRS?