cluster subpackage

Sub-package Documentation

The cluster sub-package is responsible for merging variants coming from different inputs (i.e. different tools).

Types of Output Files

expected name/suffix

file type/format

content

cluster_assignment.tab

text/tabbed

uninformative_clusters.txt

text

list of cluster ids that were dropped by annotation proximity filter

clusters.bed

bed

cluster positions

cluster-*.tab

text/tabbed

computed clusters

Algorithm Overview

  • Collapse any duplicate breakpoint pairs

  • Split breakpoint pairs by type

  • Cluster breakpoint pairs by distance (within a type)

    • Create a graph representation of the distances between pairs

    • Find cliques up to a given input size (cluster_clique_size)

    • Hierarchically cluster the cliques (allows redundant participation)

    • For each input node/pair pick the best cluster(s)

  • Output the clusters and the mapping to the input pairs

modules