variant_calls_sig: Returns variant calls given a VSeqTools_pileup object

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

Returns variant calls given a VSeqTools_pileup object

Description

Given a pileup, implements a poisson significance test to call variants.

Usage

variant_calls_sig(pu, sig = 0.01, heavy_tail = T)

Arguments

pu	a VSeqTools_pileup object returned by BAM_pileup
sig	Significance level of poisson test
heavy_tail	If T use betabinomial error distribution, otherwise use poisson error distribution.

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

References

Wang,C. et al. (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res., 17, 1195–1201,

Gerstung et al. (2011) Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications.

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