Could someone please post an example of how to calculate strand bias using samtools. I appear to be blocked from that site. Thank you.
-
-
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
-
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
Comment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment