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Old 06-04-2013, 04:59 AM   #1
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Default GATK BaseRecalibrator -output bam

I am doing my post-alignment processing on whole genomes (~40X) coverage. My aligned bam files are each ~100GB in size. After I go through all of the steps (indelrealigning, fixing mate-pairs, basereaclibrating, etc), my final output bam file after the BQSR print reads has dramatically jumped in size. They have gone from the ~100GB in size to over 120GB in size. Is this a normal occurrence and something to be alarmed by?
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gatk, printreads

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