VARNORM¶
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.
Usage¶
gor ... | VARNORM refcol altcol [ -seg | -left | -right | -trim | -span ]
Options¶
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The variant is denoted as segment, e.g. (chr,bpstart,bpstop,ref,call). |
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Normalise the variation data to the left. |
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Normalise the variation data to the right. |
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Trims the redundant bases away from the defined columns (ref + alt) |
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Max merge span. The default is 100bp, max 1Mb (crazy high!) |
Examples¶
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