Originally posted by go2seq
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samtools mpileup questions
I've got a question about using mpileup on multiple library data:
is there any difference in variant calling between
- run mpileup with multiple bam files as input,
and
- merge these bam files then run mpileup on the merged one
Thanks much for your input.Last edited by go2seq; 07-02-2011, 01:56 PM.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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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...
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