LiftOver 千人基因组(可选) 坐标转换

Liftover在线版

http://genome.ucsc.edu/cgi-bin/hgLiftOver

Liftover本地版（支持bed和gff文件）

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver

chain文件​

** Download Ensembl chain files**

• Human to Human: ftp://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/
• Mouse to Mouse: ftp://ftp.ensembl.org/pub/assembly_mapping/mus_musculus/
• Other organisms: ftp://ftp.ensembl.org/pub/assembly_mapping/

Download UCSC chain files****​

• Chain files from hg38 (GRCh38) to hg19 and all other organisms: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/
• Chain File from hg19 (GRCh37) to hg17/hg18/hg38 and all other organisms: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/
• Chain File from mm10 (GRCm38) to mm9 and all other organisms: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/

##需求hg19转化成hg18版本
 gunzip hg19ToHg38.over.chain.gz  #解压chain文件
/home/soft/liftOver /home/data/all.mp.hg19.bed /home/soft/hg19ToHg38.over.chain all.mp.hg19tohg38.bed unmapped
#liftOver [1] [2] [3] [4] 
#[1] 需要转换的文件
#[2] chain文件
#[3] 转换后的文件
#[4] 转换不成功的部分