Wgsextract

[Genetics189291]

So recently I tried to take the raw data template from dnakitstudio which was the 1240k template and replace one of the files in wgs extract, I managed to extract the data out of my cram but the issue is it causes too many no calls why is this the case 

We don’t know need a combined kit file which is more then double the snps it makes no sense especially when we are trying to merge with the dataset.