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Old 08-06-2014, 02:28 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

At first glance, it looks like the default quality filtering differs between the two, samtools 1.19 is more stringent. The ! in the quality string indicates the lower possible quality, the 1.18 version has many more than the 1.19 version, and the ! correspond to the non-consensus bases, so they are likely wrong anyway, so 1.19 is right in excluding them.
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