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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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