Make a BED file from the raw UCSC file

dbsnp-to-bed.sh

export GENOME=hg19
export SNPBUILD=131
curl -s http://hgdownload.cse.ucsc.edu/goldenPath/$GENOME/database/snp$SNPBUILD.txt.gz | \
        zcat | \
        cut -f 2,3,4,5,6,7,10,16 > dbsnp.$SNPBUILD.$GENOME.bed

head dbsnp.$SNPBUILD.$GENOME.bed
chr1	10433	10433	rs56289060	0	+	-/C	near-gene-5
chr1	10491	10492	rs55998931	0	+	C/T	near-gene-5
chr1	10518	10519	rs62636508	0	+	C/G	near-gene-5
chr1	10582	10583	rs58108140	0	+	A/G	near-gene-5
chr1	10827	10828	rs10218492	0	+	A/G	near-gene-5
chr1	10903	10904	rs10218493	0	+	A/G	near-gene-5
chr1	10926	10927	rs10218527	0	+	A/G	near-gene-5
chr1	10937	10938	rs28853987	0	+	A/G	near-gene-5
chr1	11001	11002	rs79537094	0	+	A/C	near-gene-5
chr1	11013	11014	rs28484712	0	+	A/G	near-gene-5