id_indels

Identify amino acid changes associated with indel variation. Changes associated with SNVs are identified in separate function. Used by call_mutations() function.

indel

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_indels function

<dl><dt>variant.calls</dt>
<dd>Data frame with cols POS, REF, ALT, AF, DP. Additional columns will be ignored.</dd>
<dt>ref</dt>
<dd>reference genome in "MixVir" format (from create_ref() function)</dd></dl>

Arguments

ID Indel-based Amino Acid Changes — id_indels

<dl>

<dt>variant.calls</dt>
<dd>Data frame with cols POS, REF, ALT, AF, DP. Additional columns will be ignored.</dd>


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

</dl>

id_indels: ID Indel-based Amino Acid Changes

Description

Usage

Value

Arguments