rsID2Bed

rsID2Bed is a script to convert SNP rsIDs to a list of genomics positions in a bed format: chr, position, position+1, rsID. Script is useful for quick conversion of SNPs to a bed format for downstream analysis (e.g. overlaps with bedtools).

Usage

This script will check if the working folder ~/rsID2Bed is present and if not it will create ~/rsID2Bed. Next, script will go into ~/rsID2Bed and check if dbSNP bed file for human genome hg19 is present or not, version 147 (the latest one present in the mySQL database currently), and case it is not present it will download it using mySQL from snp147Common table of hg19 dataset on genome-mysql.cse.ucsc.edu.

Note - Script rsID2Bed.sh can be placed anywhere as well as the input file, however output will be in ~/rsID2Bed

Next an akw code will perform comparison and output bed file for your input snps and save it as $1.bed, $1 being first parameter provided to the script that should be the file name containing SNPs.

Output file will be placed in ~/rsID2Bed

MySQL download will produce a file snp147Common.bed, with 14,815,821 SNPs:

<pre> head snp147Common.bed chr1 10177 10177 rs367896724 chr1 10352 10352 rs555500075 chr1 11007 11008 rs575272151 chr1 11011 11012 rs544419019 chr1 13109 13110 rs540538026 chr1 13115 13116 rs62635286 chr1 13117 13118 rs62028691 chr1 13272 13273 rs531730856 chr1 13417 13417 rs777038595 chr1 14463 14464 rs546169444 mpjanic@zoran:~/rsID2Bed$ wc -l snp147Common.bed 14815821 snp147Common.bed </pre>

Running

To run the script type:

<pre> chmod 775 rsID2Bed.sh ./rsID2Bed.sh path/to/file </pre>

Prerequisites

MySQL

Example

<pre> cat SNP.file rs575272151 rs62028691 rs546169444 rs541940975 rs4690 rs201327123 rs11586607 rs62636497 rs369786760 rs143379270 rs764954080 rs762420258 ./rsID2Bed.sh SNP.file cat SNP.file.bed chr1 11007 11008 rs575272151 chr1 13117 13118 rs62028691 chr1 14463 14464 rs546169444 chr1 14603 14604 rs541940975 chr1 14672 14673 rs4690 chr1 14676 14677 rs201327123 chr1 15210 15211 rs11586607 chr1 15273 15274 rs62636497 chrX 155258430 155258431 rs369786760 chrX 155258653 155258654 rs143379270 chrX 155259767 155259767 rs764954080 chrX 155259783 155259783 rs762420258 chrY 59361436 59361437 rs369786760 chrY 59361659 59361660 rs143379270 chrY 59362773 59362773 rs764954080 chrY 59362789 59362789 rs762420258 </pre>