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Weird problem with the Unified Genotyper leaving out individuals
I have been running the GATK pipeline on 114 subjects. I have reduced the bam files (after local realignment and BQSR) using reduced reads and incorporate all 114 bam files into my UnifiedGenotyper command. The problem is I only get 113 out, one particular individual never comes through (not the first in the list or last). I have tried looking at the bam files in IGV and they look fine. I have tried renaming the bam file of the one individual left out - this doesn't help. I have had others look at my command line for errors related to that individual and they can't see anything. Finally, I took the exact same command line and just removed all other bam inputs. This gave me a vcf file with just the 1 individual. When I compare VCF files of single individuals to the one I produced with all subjects the variants called are slightly different. Do you have any idea for me on how to be able to use the UnifiedGenotyper on all of my subjects?