chromothripsis

Chromothripsis Analysis (in progress)

Module authors : Yang Yang (@yangyangclover) Modifications in progress by Laura Egolf (@LauraEgolf)

This module runs ShatterSeek, classifies chromothripsis regions, and visualizes the results.

Inputs from data download

• independent-specimens.wgs.primary-plus.tsv
• pbta-sv-manta.tsv
• pbta-cnv-consensus.seg

Order of scripts in analysis

01-process-sv-file.R : This script reformats SV files for ShatterSeek input.

02-shatterseek.R : This script runs ShatterSeek and classifies chromothripsis regions as high or low confidence based on criteria recommended by the authors. [Modifications ongoing]

More scripts will be added.