View Single Post
Old 08-06-2014, 03:28 PM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

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.
swbarnes2 is offline   Reply With Quote