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Forum: Bioinformatics 08-07-2014, 08:00 AM
Replies: 3
Views: 1,649
Posted By sscd
Searching around a bit, the SAMtools v0.1.18...

Searching around a bit, the SAMtools v0.1.18 behavior when mpileup uses the Q flag is documented here:

https://github.com/samtools/samtools/wiki/FAQ
Forum: Bioinformatics 08-07-2014, 07:46 AM
Replies: 3
Views: 1,649
Posted By sscd
@swbarnes, thanks for the quick reply. That...

@swbarnes, thanks for the quick reply. That certainly explains what I am seeing. I inspected a larger sample and found SAMtools v01.19 is indeed filtering out the read bases with quality < 13.
...
Forum: Bioinformatics 08-06-2014, 12:28 PM
Replies: 3
Views: 1,649
Posted By sscd
Pileup differences with different SAMtools versions

Hello,

Generating pileups of bacterial data sets with SAMtools 0.1.18 and 0.1.19, I have noticed differences in the pileup files. Version 0.1.18 produces pileups with greater depth. In both...
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