Make BED File from Illumina Manifest

To compare coverage across SNP arrays, it is handy to convert Illumina manifest files into .bed files for easy manipulation.  To do this, the first step is to download the desired manifest file from the Illumina website.  Here is a site that lists the downloads available for each array they support.  Once you find the array select the manifest file (I usually choose the CSV file) and download from the browser or copy the link and use wget.  Here is an example for the Methylation450 array:

wget http://supportres.illumina.com/documents/downloads/productfiles/humanmethylation450/humanmethylation450_15017482_v1-2.csv

view raw get_manifest.sh hosted with ❤ by GitHub

Next, look at the manifest file and determine what columns are for the chromosome and the base pair coordinates (usually some name like Chr and Coordinate).  Put these column numbers into the below line of UNIX code and you will have a .bed file from the manifest file.  Here I am making a file only for the X chromosome, but this can be modified to fit your respective needs as well.

cut -d "," -f15,16 humanmethylation450_15017482_v1-2.csv | sed -e 's/,/\t/' | grep "^X" | sort -n -k2 | awk 'BEGIN{OFS="\t"};{print "chr"$1,$2,$2}' > chrX_HumanMethylation450.bed

view raw make_bed.sh hosted with ❤ by GitHub

You should be all set with a .bed file from your manifest file.  Just ensure that when you are making comparisons you are using the correct genome build.