make-simrep-micsat-bed.sh

# download simple repeats from UCSC and convert to BED
curl -s http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/simpleRepeat.txt.gz \
    | gzcat \
    | cut -f 2-5 \
    > simrep.hg19.bed

# download microsatellites from UCSC and convert to bed
curl -s http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/microsat.txt.gz \
    | gzcat \
    | cut -f 2-5 \
    > micsat.hg19.bed

# merge the twain
cat simrep.hg19.bed micsat.hg19.bed \
    | sort -k1,1 -k2,2n \
    | bedtools merge -i - -c 4 -o collapse \
    > simrep.micsat.merge.hg19.bed

# bgzip and tabix
bgzip simrep.micsat.merge.hg19.bed
tabix -p bed simrep.micsat.merge.hg19.bed.gz

#profit