I am using the GATK UnifiedGenotyper to generate a gVCF file based using the Emit_All_Stites option.
The problem I have is that if I have a single chromosome BAM such as BAM for only say chromosome 3 and I want gVCF data for only chromosome 3, is it possible to do that? So I want a gVCF file with variant and non variant sites only for chromosome 3
Right now when I run GATK then it starts processing all the chromosomes. Is there a way to only generate gVCF data for one chromosome even if genome truly means all the chromosomes?