PhaseDel

PhaseDel is a Java-based variant caller designed for detecting somatic deletions from single-cell whole-genome sequencing (scWGS) data. It is highly specialized for discriminating genuine somatic focal deletions (several bases to kilo-bases in length) from excessive SV-like artifacts, which are inevitably occurring during single-cell whole-genome amplification. PhaseDel accurately detects such true deletions based on the linkage information between deletion breakpoints and nearby germline heterozygous SNP sites. The important features of PhaseDel are:

• Accurate identification of somatic focal deletions at single-base-pair resolution in scWGS using phasing information
• Estimation of the genome-wide somatic deletion rate for a given cell with the controlled FDR level
• Characterization of underlying DSB repair mechanisms for identified deletion candidates

A more detailed description of the tool is provided in the [[wiki]] tab.