deletion_call: Creates a StructuralVariant object, linking genomic intervals...

In cancer-genomics/trellis: Somatic structural variant analysis

Creates a StructuralVariant object, linking genomic intervals (deletions) to read pairs supporting the rearrangement

Description

Identifies somatic, focal hemizygous and homozygous deletions, then links these deletions with properly and improperly paired reads.

Usage

deletion_call(preprocess, gr_filters, param = DeletionParam())

Arguments

preprocess	A list object generated by preprocessData
gr_filters	A GRanges object of germline CNVs and sequence-based filters identified by low mappability and/or GC content
param	A DeletionParam object

See Also

See germlineFilters for identifiying somatic deletions.

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.