2.1.3 Merging: merge synthenic blocks

The Merge filter fuses consecutive blocks based on their coordinates. Blocks will be fused only if the sequences from a specified set of species can be considered as syntenic. Two sequences are considered as syntenic if:

• they are from the same species
• they are from the same chromosome
• they are from the same strand
• they are distant by less than a defined threshold (the start of sequence 2 - the end of sequence 1 < threshold in bp).

Synopsis:

maf.filter=                                 \
    [...],
    Merge(                                  \
        species=(species1, species2, etc),  \
        dist_max=0,                         \
        ignore_chr=(Random,Unknown),        \
        rename_chimeric_chromosomes=yes),   \
    [...]

Arguments:

species=(species1, species2, etc)

A coma separated, within parentheses, list of species. These species only will be used for the synteny check. Other species will be concatenated in any situation, and their coordinates removed.

dist_max={int}

Maximum distance (in nt) to consider sequences as syntenic. If dist_max is greater than 0, sequences will be filled with ’N’ to preserve coordinates when they are fused.

ignore_chr={none | (list)}

An optional parenthetic list of chromosomes to ignore (typically "Unknown", or "Random", etc.). Sequences annotated with such chromosomes will not be checked for synteny and the corresponding block will not be fused.

rename_chimeric_chromosomes={boolean}

When distinct chromosomes are merged (in non specified species), their names are concatenated. If this option is set to "yes", then merged chromosomes will be renamed as "chimtigXXX" where XXX is a number auto-incremented for each species.