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Old 03-11-2011, 06:53 AM   #4
Jon_Keats
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279
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In the case of this error that I discovered trying to get picard to remove the duplicates I found that samtools did not correct the SO header while picard did, not sure why that occurs as a bwa generated bam file when sorted with samtools gets the right header.
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