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

README.md

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:

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

Running

To run the script type:

chmod 775 rsID2Bed.sh 
./rsID2Bed.sh path/to/file

Prerequisites

MySQL

Example

 
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
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