This page contains the source strand
aligned files for Illumina genotyping chips. For a detailed explanation of the files please refer to the Strand Home page
If you have a chip and/or genome build that is not listed here please contact
me, Will Rayner (The standard strand files, on the strand
home page, assume the data has been exported on the TOP strand, the files
below are for use when the genotypes have been exported using the Illumina
Source (SRC) strand. This is one of the three possible strand alignment
export options (The others being TOP and Ilmn), it is in my experience the most common
alternative strand, and whilst there are other
options such as FORWARD and PLUS, these are ultimitely either Source or
Ilmn aligned.
These files only contain the .strand file, if you require the .miss and
multiple files these can be obtained from the corresponding TOP strand zip
available on the strand home page.
If you are unsure of the alignment to use then please contact me at the
above email address
The script developed by Neil Robertson for updating the chromosome,
position and strand of binary ped files using these source strand and
position files can be downloaded here:
update_build.sh
Usage is:
update_build.sh <bed-file-stem> <strand-file>
<output-file-stem>
where:
<bed-file-stem>
|
is the name of your binary ped
set minus the .bed, .bim or .fam extension
|
<strand-file>
|
is appropriate strand file for you
chip and current strand orientation (TOP, SOURCE, ILMN)
|
<output-file-stem>
|
is the name of the new output
file to create again minus the .bed, .bim or .fam extension
|
Allele Updates
If your genotypes are represented as A/B then the files present
here allow you to update the alleles
from A/B to TOP strand A, C, G, T calls, if the chip you are using is
not listed contact me and I can create these files.