DBS_conclusion_1_row: Examine 1 row of a DBS-only VCF that was already processed by...

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

Description

Examine 1 row of a DBS-only VCF that was already processed by Slice2ReadSupport to decide if the DBS is likely real.

Usage

DBS_conclusion_1_row(row, germlineCutOff = 0.1, max.half.support.T.reads = 1)

Arguments

row	One row of a DBS VCF (as a data.frame) already processed by Slice2ReadSupport (so that the fields vcf$NreadSupport and vcf$TreadSupport are populated).
germlineCutOff	If this proportion of normal reads show one or the other variant (or both variants), consider this a germline variant or partial germline variant.
max.half.support.T.reads	Do not tolerate more than this number of reads in the tumor that support one but not both mutated positions.

Value

A character string indicating the conclusion about the putative DBS.

steverozen/DBSverify documentation built on Dec. 23, 2021, 5:34 a.m.