Variant data

Variant data may be obtained either by importing variants from files (e.g. gvf or vcf files - as described in Import tracks), by downloading variants from external databases (e.g. dbSNP, HapMap, 1000genomes or COSMIC - (described in Import tracks)) or by calling variants on read tracks or read mappings using the CLC Probabilistic Variant Detection (Probabilistic variant detection) or the Quality-based Variant Detection (Quality-based variant detection) tools.

Variant types include SNVs, MNVs, insertions, deletions or replacements. They may be presented either in a variant track (see figure 26.32) or in an annotated variant table (see figure 26.35).


Subsections