seq_call: Function to produce a sequencing read at one locus with...

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

It uses formula p(D=g|G_1=g)=1-e,p(D=other\ call|G_1=g)=e/3 to generate the read for a given genotype G_1 and error rate e. It is called from the generate_seqdata functions.

Usage

seq_call(genotype, error, ndepth)

Arguments

genotype	vector of two alleles for a given genotype, ie. genotype CT is given as ('C', 'T')
error	vector of sequencing errors, length of this vector is the same as read depth (ndepth).
ndepth	the read depth (integer)

Value

a row vector of sequence reads consisting of 'A','G','T' or 'C' for a single variant with length the same as read depth (ndepth).

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.