make.blacklist: Make a list of regions of the genome in which there is...

In mskilab/fragCounter: GC mappability correction and segmentation

Make a list of regions of the genome in which there is coverage in the normal samples

Description

Look at all available normal samples and find regions where some percentage of all normal samples have at least 1 read

Usage

make.blacklist(pairs, cutoff = 0.9, mc.cores = mc.cores)

Arguments

pairs	string Input data.table with columns 'pair' and 'bam' corresponding to the sample name and bath to normal bam
cutoff	double Threshold for what percentage of normal samples must have reads for the region to be included
mc.cores	integer Number of cores to use

Value

Data.table of regions to include when calculating corrected reads

Author(s)

Trent Walradt

mskilab/fragCounter documentation built on Jan. 27, 2024, 2:35 p.m.