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ReducedReads - different number of SNPs

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

Best Answer


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