Lift genome positions
Genome positions are best represented in BED format. UCSC provides tools to convert BED file from one genome assembly to another.
Binary liftOver tool
We need liftOver binary from UCSC and hg18 to hg 19 chain file.
Provide BED format file (e.g. input.bed)
NOTE: Use the 'chr' before each chromosome name
chr1 743267 743268 rs3115860
chr1 766408 766409 rs12124819
chr1 773885 773886 rs17160939
Run liftOver:
(1) download liftOver http://hgdownload.cse.ucsc.edu/admin/exe/
(2) chmod +x liftOver
(3) download chain file http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/
(4) prepare input bed file (chr start end others ...)
(5) run liftOver
./liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed
unlifted.bed file will contain all genome positions that cannot be lifted. The reason for that varies. See Various reasons that lift over could fail
REF:
http://www.zilhua.com/906.html （使用方法）
http://genome.sph.umich.edu/wiki/LiftOver （wiki）
http://www.cnblogs.com/foreverycc/p/3170807.html （使用方法）
http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ （liftOver的chain文件）
http://hgdownload.cse.ucsc.edu/admin/exe/ （下载 liftover； http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver ）