DBSConclusion: Examines every row of of DBS VCF already processed by...

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

Description

Examines every row of of DBS VCF already processed by Slice2ReadSupport and decides which DBSs are likely real.

Usage

DBSConclusion(vcf, germlineCutOff = 0.2, max.half.support.T.reads = 1)

Arguments

vcf	An in memory 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 VCF with the field DBSconclusion populated.

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