Question: VCFtools LD calculations only for pairs that include a single SNP of interest
1
gravatar for Scott
4.7 years ago by
Scott80
Canada
Scott80 wrote:

I would like to calculate LD statistics for a VCF file using VCFtools. For the 1Mb window I am interested in, even using a R^2 minimum of 0.2, it is taking quite a bit of time to calculate these statistics.

I am ultimately only interested in LD statistics that include a single SNP of interest. Is there a way to have VCFtools compute LD stats only for pair-wise comparisons that include my SNP of interest, but still over the whole 1Mb region?  

My understanding is that the "ld-window" options can define only the entire region to use, so they are not useful for this application. 

ADD COMMENTlink modified 4.7 years ago by Adam990 • written 4.7 years ago by Scott80
2
gravatar for Adam
4.7 years ago by
Adam990
United States
Adam990 wrote:

The yet-to-be-released version of vcftools (in the SVN) has a new option that allows you to do something like this. The option is called --hap-r2-positions, and allows you to specify a list of sites to be tested against all other sites for LD. To use the option, you just use --hap-r2-positions <positions_filename>.

ADD COMMENTlink written 4.7 years ago by Adam990

That's useful, and means the conversion to plink is now unnecessary, cheers.

ADD REPLYlink written 4.7 years ago by smilefreak420
1
gravatar for smilefreak
4.7 years ago by
smilefreak420
New Zealand
smilefreak420 wrote:

Hi Scott,

Plink has this functionality, you could use VCFtools to extract your region of interest and convert to the plink format.

http://vcftools.sourceforge.net/documentation.html#plink

Then use Plink for the ld calculations for your SNP, the command would look similar to this one below, which I copied from the plink documentation.

 

    plink --file mydata 
          --r2 
          --ld-snp rs12345 
          --ld-window-kb 1000 
          --ld-window 99999 
          --ld-window-r2 0

http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml

ADD COMMENTlink written 4.7 years ago by smilefreak420
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