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ReducedReads - different number of SNPs

volaviivolavii Member Posts: 17

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

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