GenomeComb

liftsample

Format

cg liftsample sampledir resultdir liftoverfile dbdir

Summary

Use liftover to convert the files from a sample (variant, region, ...) from one build to another

Description

Converts a sample from one build to another (using liftover from ucsc). 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

sampledir
file in sft format (with variant data)
resultdir
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