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/ （下載 liftover； http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver ）

http://genome.ucsc.edu/FAQ/FAQformat.html#format1 (bed文件格式)

liftover[裝載自http://www.cnblogs.com/emanlee/p/5064630.html]