Copy number variant calling and recovery

A computer system comprising:

• a memory;
• and
• a processor in communication with the memory, wherein the computer system is configured to perform a method for improved calling of copy number variants in a genomic sequence, the method comprising:
• obtaining genetic sequence variant data comprising records indicating at least one structural variant (SV) and records indicating at least one copy number variant (CNV) in the genomic sequence;
• determining, based on an initial CNV indicated in the genetic sequence variant data and on at least one initial SV indicated in the genetic sequence variant data, an SV-informed CNV call as an updated version of the initial CNV, wherein the determining uses information from the at least one initial SV to determine a start breakpoint position and an end breakpoint position for the SV-informed CNV call, at least one of the start breakpoint position and end breakpoint position being updated, informed by the at least one initial SV, in comparison to a corresponding start breakpoint position and/or end breakpoint position of the initial CNV;
• and
• writing the determined SV-informed CNV call as one or more records in a genetic sequence variant data file.

A computer program product comprising:

• a computer readable storage medium readable by a processing circuit and storing instructions for execution by the processing circuit for performing a method for improved calling of copy number variants in a genomic sequence, the method comprising:
• obtaining genetic sequence variant data comprising records indicating at least one structural variant (SV) and records indicating at least one copy number variant (CNV) in the genomic sequence;
• determining, based on an initial CNV indicated in the genetic sequence variant data and on at least one initial SV indicated in the genetic sequence variant data, an SV-informed CNV call as an updated version of the initial CNV, wherein the determining uses information from the at least one initial SV to determine a start breakpoint position and an end breakpoint position for the SV-informed CNV call, at least one of the start breakpoint position and end breakpoint position being updated, informed by the at least one initial SV, in comparison to a corresponding start breakpoint position and/or end breakpoint position of the initial CNV;
• and
• writing the determined SV-informed CNV call as one or more records in a genetic sequence variant data file.