vcf_to_mixvir

Create data frame with relevant contents of VCF

Tool for exploring DNA and amino acid variation and inferring the presence of target lineages from microbial high-throughput genomic DNA samples that potentially contain mixtures of variants/lineages. MixviR was originally created to help analyze environmental SARS-CoV-2/Covid-19 samples from environmental sources such as wastewater or dust, but can be applied to any microbial group. Inputs include reference genome information in commonly-used file formats (fasta, bed) and one or more variant call format (VCF) files, which can be generated with programs such as Illumina's DRAGEN, the Genome Analysis Toolkit, or bcftools. See DePristo et al (2011) <doi:10.1038/ng.806> and Danecek et al (2021) <doi:10.1093/gigascience/giab008> for these tools, respectively. Available outputs include a table of mutations observed in the sample(s), estimates of proportions of target lineages in the sample(s), and an R Shiny dashboard to interactively explore the data.

Michael Sovic

MixviR

Analysis and Exploration of Mixed Microbial Genomic Samples

Francesca Savona

Zuzana Bohrerova

Seth Faith

vcf_to_mixvir function

<dl><dt>infile</dt>
<dd>Path to a vcf file that must contain "DP" and "AD" flags in the FORMAT field.</dd>
<dt>max.vcf.size</dt>
<dd>Max memory usage (in bytes) allowed when reading in vcf file (from vcfR).</dd></dl>

Arguments

Convert Sample VCF to MixviR Input Format — vcf_to_mixvir

<dl>

<dt>infile</dt>
<dd>Path to a vcf file that must contain "DP" and "AD" flags in the FORMAT field.</dd>


<dt>max.vcf.size</dt>
<dd>Max memory usage (in bytes) allowed when reading in vcf file (from vcfR).</dd>

</dl>

vcf_to_mixvir: Convert Sample VCF to MixviR Input Format

Description

Usage

Value

Arguments

Examples