UnifiedGenotyper removed samples?
Hello everyone. I'm using GATK to call SNPs on data set of 54 samples, however, after I used UnifiedGenotyper I noticed that my vcf file now contains 24 samples, so 30 samples were removed. I used dcov 200 and emit-all-sites. It is normal that some samples were removed from the data set in the final vcf?. Thanks for your response.