Friday, 18 November 2011

VCFtools BEDtools compare, intersect, merge

A Good computational biologist is only as good as the tools he uses (or maybe how good he is at google) rofl kidding ...
Life is always easier when you find the correct tool.
I also adopt the path of least resistance when trying to solve problems that are more common than I imagine.
There's always the good old linux tools for comparing SNPs called from different programs / options

   grep | sed | awk | cut | diff | comm

and if you are working with NGS data, you most probably already have samtools installed on your system and you might have used bcftools
Did you also know that there's also a (unrelated) set of tools called vcftools?

The VCFtools package is broadly split into two sections: 

Then there's  also the highly used BEDTools

which I highly recommend to keep as part of your tools collection. Check out the link below

Do watch out for this 'oversight' in vcftools as pointed out in seqanswers.
Overlap number discrepancy between VCFTools and BEDTools

UsageExamples of common usage.   Featured

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Datanami, Woe be me