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Could someone please post an example of how to calculate strand bias using samtools. I appear to be blocked from that site. Thank you.
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Strand bias is output in VCF/BCF files, so the way to calculate that would just be to call SNPs (just google for the exact commands, if you can't connect to the site, then just look at google's cached copy). -
strand bias and samtools
I am blocked using the cache version as well. Can you please post an example? Thank you.Comment
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Your IT people block google?!?! You might want to move, or just have them fired for utter incompetence (though "pebcak" is the more likely culprit).
The example from the sourceforge page is:
Code:samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
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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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