extractCoverageFromVcf

Extract read counts from VCF file 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

extractCoverageFromVcf function

<dl><dt>vcfFileName</dt>
<dd>Path of the VCF file.</dd>
<dt>ADFieldIndex</dt>
<dd>Index of the AD field of the sample field. For example,
if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).</dd></dl>

Arguments

Extract read counts from VCF — extractCoverageFromVcf

<dl>

<dt>vcfFileName</dt>
<dd>Path of the VCF file.</dd>


<dt>ADFieldIndex</dt>
<dd>Index of the AD field of the sample field. For example,
if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).</dd>

</dl>

extractCoverageFromVcf: Extract read counts from VCF

Description

Usage

Value

Arguments

Examples