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 Basic Variant Detection (Basic Variant Detection), Fixed Ploidy Variant Detection (Fixed Ploidy Variant Detection), or the Low Frequency Variant Detection (Low Frequency Variant Detection) tools.

Variant types include SNVs, MNVs, insertions, deletions or replacements. They may be presented either in a variant track (see figure 27.46) or in an annotated variant table (see figure 27.49).


Subsections