239
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→User-supplied LD
LocusZoom by default automatically computes LD between the reference SNP and all other SNPs within each region to be plotted. However, in some instances, you may wish to provide your own file with LD information. This can be done with the <code>--ld</code> option, which requires a file of the following format:
LocusZoom by default automatically computes LD between the reference SNP and all other SNPs within each region to be plotted. However, in some instances, you may wish to provide your own file with LD information. This can be done with the <code>--ld</code> option, which requires a file of the following format:
<br>
{| width="75%" cellspacing="0" cellpadding="5" border="1"
{| width="75%" cellspacing="0" cellpadding="5" border="1"
|-
|-
| rsquare || r<sup>2</sup> between snp2 (reference SNP) and snp1.
| rsquare || r<sup>2</sup> between snp2 (reference SNP) and snp1.
|}
|}
<br>
The file should be whitespace delimited.
The file should be whitespace delimited.
