GenomeComb
cg svmulticompar ?options? file svfile ...
Compare multiple structural variant files
This command is used to create multi sv compar_files. These are tab separated files indicating structural variants present in one or more samples. As structural variant (sv) calls are usually imprecise, the sv (of different samples) are approximately matched: Begin, end or alt values do not have to match exactly. The global variant features (chromosome, begin, end, type, ref, alt) are taken from the first sample the variant is seen in. (so there can be small differences due to order of samples given) The values for begin, end and alt values of each sample are kept as lbegin-sample, lend-sample and lalt-sample.
SVs match if they are the same type (trans and bnd are considered the same type for this) and begin, end and alt differences are within the given margins. Begin (and end) difference are calculated by the number of bases between begin positions (and end positions), and must (in general) not be more than margin (default 30) bases. For deletions and inversions lmargin (default 300) is used, but they also must have at least minoverlap (default 75%) percent (vs largest SV) to match. Insertions use margin (30) from begin and end differences, and pct overlap (but only based on size, sequence is not compared) must be at least minoverlap (default 75%). For special insertions (alt starts with <) alts must match completely. For translocations or breakends tmargin (default 300) is used as a limit for begin and end differences; They must also link to the same chromosome, and difference in position of the link may also be maximaly tmargin.
Variants