cg liftover variantfile resultfile liftoverfile
Use liftover to convert a variant file from one build to another
Converts a variantfile from one build to another based on a liftover file. The liftover file is a tab separated file indicating which regions in the source genome (chromosome,begin,end,strand) shoud be converted to which regions in the destination genome (destchromosome,destbegin,destend,deststrand). If a UCSC liftover chainfile is given as a liftover file, it is converted into a liftover file using the command "cg liftchain2tsv chainfile liftoverfile".
cg liftover tries to correct the variants if there are changes in strand or reference. It will adapt the fields ref, alt, sequenced*, zyg* according to the changes. It uses the file <liftoverfile base>.refchanges.tsv for this. This file must contain the differences in reference sequence between the source and destination genome, and can be generated using the command "cg liftfindchanges srcgenome destgenome liftoverfile" if not available.
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. Regions that were not present in the source genome will obviously not have variants.