Used in: gor only


The VARNORM command normalises the variation data in a gor stream to the left or right. The column containing the reference and alternate allele must be specified. If neither -left nor -right is specified, then left normalisation is default.

If the -trim command is used, then any redundant bases in the representations of insertions or deletions will be deleted (i.e. deletions will be represented by empty cells in Call - or in Reference in the case of insertions).

By default, normalisation is run automatically as part of a VARJOIN command, however, if variants need to be grouped (e.g. for counting or generating horizontal data) the InDels must be normalized. For very large InDels a high span may be needed, however, we don’t recommend excessive span. Consider then the use of pre-normalized data and the -norm option in VARJOIN. The system can be configured to default on -norm behaviour for VARJOIN.


gor ... | VARNORM refcol altcol [ -seg | -left | -right | -trim | -span ]



The variant is denoted as segment, e.g. (chr,bpstart,bpstop,ref,call).


Normalise the variation data to the left.


Normalise the variation data to the right.


Trims the redundant bases away from the defined columns (ref + alt)


Max merge span. The default is 100bp, max 1Mb (crazy high!)


gor -p chr1:723798-723802 #dbsnp# | CALC oldpos pos | VARNORM -right reference allele
gor #dbsnp# | VARNORM -left #3 #4 | GROUP 1 -gc #3,#4 -count | WHERE allcount > 1 | TOP 2