Lift genome positions

Genome positions are best represented in . UCSC provides tools to convert BED file from one genome assembly to another.

Binary liftOver tool

We need  from UCSC and .

Provide BED format file (e.g. input.bed)

NOTE: Use the 'chr' before each chromosome name

chr1    743267  743268  rs3115860chr1    766408  766409  rs12124819chr1    773885  773886  rs17160939

Run liftOver:

(1) download liftOver   (2) chmod +x liftOver (3) download chain file   (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 

 

 

REF:

 （使用方法）

  （wiki）

 （使用方法）

 （liftOver的chain文件）

 （下载 liftover； r ）

  (bed文件格式)