variant_calls_cutoff: Returns variant calls given a VSeqTools_pileup object

variant_calls_cutoffR Documentation

Returns variant calls given a VSeqTools_pileup object

Description

Given a pileup, variants with variability above min_freq are identified. This is a simple variant caller which is much faster than VPhaser2, but cannot call low frequency variants with precision since phasing information is not used

Usage

variant_calls_cutoff(pu, min_freq = 0.03)

Arguments

pu

a VSeqTools_pileup object returned by BAM_pileup

min_freq

Minimum frequency above which a variant is called.

Value

A VSeqTools_variant_call object which inherits the data.frame class. VSeqTools_variant_call objects are data.frames with columns pos, A, C, G, T, d, i. pos gives the position on the reference. Entries in other columns are logical depending on whether associated variant/deletion/insertion is called

Warning: Currently uses the df data.frame in VSeqTools_pileup object. Needs to be extended to allow for different strands.


SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.