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how to use samtools to view the .snp file format generated from MAQ?
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Samtools is used to view alignments in the SAM/BAM format. Have you taken a look at the tools that come with MAQ?Originally posted by johnsequence View Post -
Thanks for reply, but I did not know which tools in MAQ should be used to view the output (final snp file) generated from MAQ because this is first time I handled this type of data. Could you please describe its specificity? Thanks.Comment
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I googled and found the MAQ manual. The .snp format is described there.Originally posted by johnsequence View PostComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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