extractCoverageFromTxt

Extract read counts from tab-delimited text files of a single
 sample.

Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.

Joe Zhu

DEploid

Deconvolute Mixed Genomes with Unknown Proportions

Jacob Almagro-Garcia

Gil McVean

University of Oxford 

Yinghan Liu

CodeCogs Zyba Ltd

Deepak Bandyopadhyay

Lutz Kettner

extractCoverageFromTxt function

<dl><dt>refFileName</dt>
<dd>Path of the reference allele count file.</dd>
<dt>altFileName</dt>
<dd>Path of the alternative allele count file.</dd></dl>

Arguments

Extract read counts from plain text file — extractCoverageFromTxt

<dl>

<dt>refFileName</dt>
<dd>Path of the reference allele count file.</dd>


<dt>altFileName</dt>
<dd>Path of the alternative allele count file.</dd>

</dl>

extractCoverageFromTxt: Extract read counts from plain text file

Description

Usage

Value

Arguments

Examples