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Old 08-23-2017, 04:30 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 823
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Samtools mpileup has its own INDEL correction, which may be influencing the results that you're seeing. You could try skipping this (option `-I) and seeing if it changes the results.
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