listGenomeFilters: Genomic filters for the somatic amplicon analysis

In cancer-genomics/trellis: Somatic structural variant analysis

Genomic filters for the somatic amplicon analysis

Description

When paired normal samples are unavailable, we use germline lymphoblast cell lines to identify CNVs and outliers that are common in the germline and unlikely to be somatic. Filters relevant for the somatic amplicon analysis include germline CNVs, centromeric regions, and assembly gaps. We additionally defined a 'paired bin filter' containing bins that appear to be linked by improperly spaced reads in the lymphoblast samples. Aberrantly spaced linked bins could indicate a new junction in the lymphoblast cell line or a sequencing artifact.

Usage

listGenomeFilters(genome = c("hg19", "hg18"))

Arguments

genome

length-one character vector specifying UCSC genome build

Details

REFACTORING: Separate filters from the parameter list. Create a single filter object for both the amplicon and deletion analyses. * See germline_filters. Do we still need this? *

Value

a named list

See Also

germline_filters

Examples

filters <- listGenomeFilters("hg19")

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.