GenomeComb

liftregion

Format

cg liftregion regionfile resultfile liftoverfile

Summary

Use liftover to convert a region file from one build to another

Description

Converts a regionfile from one build to another (using liftover from ucsc). The region are lifted as separate 1 base long parts, meaning that a region can be split or miss parts. A liftover conversion is likely to cause loss of information: not all variants/regions can be properly converted. Variants that were dropped in the conversion, will be available in resultfile.unmapped.

Arguments

regionfile
file in tsv format (with region data)
resultfile
resulting converted file
liftoverfile
liftover file guiding the conversion, e.g. hg18/hg18ToHg19.over.chain to convert from hg18 to hg19, and hg19/hg19ToHg18.over.chain to convert from hg19 to hg18

Category

Conversion