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Hello, I am using the latest GATK Unified Genotyper (UG) software for my BWA aligned reads (paired-end). 1. BWA: default parameters 2. markDuplicates (PICARD) and realignment (GATK) 3. UnifiedGenotyper default values except: stand_call_conf 30.0, stand_emit_conf 10.0 When I use the ReducedBam with UG, I get 2,247,468 SNPs When I use the Bam without ReducedReads UG gives me 2,245,966 SNPs
I used BEDTOOLS to compare both files: 2,229,901 shared SNPs 17,567 only identified with the ReducedReads Bam 16,065 only identified with the non ReducedReads Bam
Do you have an idea, what happend here? Many thanks in advance