id_snps

Identify amino acid changes associated with single nucleotide variation. Changes associated with indels are identified in separate function. Used by call_mutations() function.

SNPs

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

id_snps function

<dl><dt>variant.calls</dt>
<dd>Data frame with cols POS, REF, ALT, AF (alt freq), DP (total read depth).</dd>
<dt>ref</dt>
<dd>reference genome in "MixVir" format (from create_ref() function)</dd>
<dt>code.num</dt>
<dd>Number defining the genetic code to use for translation</dd></dl>

Arguments

ID SNV-based Amino Acid Changes — id_snps

<dl>

<dt>variant.calls</dt>
<dd>Data frame with cols POS, REF, ALT, AF (alt freq), DP (total read depth).</dd>


<dt>ref</dt>
<dd>reference genome in "MixVir" format (from create_ref() function)</dd>


<dt>code.num</dt>
<dd>Number defining the genetic code to use for translation</dd>

</dl>

id_snps: ID SNV-based Amino Acid Changes

Description

Usage

Value

Arguments