snpeff_vcf

An example dataset containing 14 variants from 49 genome samples that has
been annotated using snpeff.

datasets

Standardize the pre-processing of genomic variants before
performing a bacterial genome-wide association study (bGWAS). 'prewas'
creates a variant matrix (where each row is a variant, each column is a
sample, and the entries are presence - 1 - or absence - 0 - of the variant)
that can be used as input for bGWAS tools. When creating the binary variant
matrix, 'prewas' can perform 3 pre-processing steps including: dealing with
multiallelic SNPs, (optional) dealing with SNPs in overlapping genes, and
choosing a reference allele. 'prewas' can output matrices for use with both
SNP-based bGWAS and gene-based bGWAS. This method is described in Saund et
al. (2020) <doi:10.1099/mgen.0.000368>. 'prewas' can also provide
gene matrices for variants with specific annotations from the 'SnpEff'
software (Cingolani et al. 2012).

Katie Saund

prewas

Data Pre-Processing for Bacterial Genome-Wide Association
Studies

Zena Lapp

Stephanie Thiede

snpeff_vcf function

vcfR class object with three sections:<dl class="dl-horizontal">
 <dt>meta</dt><dd>The metadata for the VCF file including the file format version
 number</dd>
 <dt>fix</dt><dd>A character matrix with 14 rows and 8 columns. Contains
 information on chromosome (CHROM), genome position (POS), reference genome
 allele (REF), and alternative allele (ALT). Information column (INFO)
 contains a field called "ANN" which provides the snpeff annotation
 including predicted functional impact of the variant on the protein
 function.</dd>
 <dt>gt</dt><dd>A character matrix with 14 rows and 49 columns. Presence/absence
 for each variant defined in fix. Colnames are sample IDs.</dd>
 </dl>

Format

Nucleotide variants in example genome samples with snpeff annotations. — snpeff_vcf

vcfR class object with three sections:<dl class='dl-horizontal'>
 <dt>meta</dt><dd>The metadata for the VCF file including the file format version
 number</dd>
 <dt>fix</dt><dd>A character matrix with 14 rows and 8 columns. Contains
 information on chromosome (CHROM), genome position (POS), reference genome
 allele (REF), and alternative allele (ALT). Information column (INFO)
 contains a field called "ANN" which provides the snpeff annotation
 including predicted functional impact of the variant on the protein
 function.</dd>
 <dt>gt</dt><dd>A character matrix with 14 rows and 49 columns. Presence/absence
 for each variant defined in fix. Colnames are sample IDs.</dd>
 </dl>

snpeff_vcf: Nucleotide variants in example genome samples with snpeff annotations.

Description

Usage

Arguments

Format