hard_filter

This function requires a vcfR object as input.
The user can then specify the minimum value for depth of coverage required to retain
a called genotype (must be numeric).
Additionally, the user can specify a minimum genotype quality required to retain
a called genotype (again, must be numeric).

Is designed to interactively and reproducibly visualize and filter SNP
(single-nucleotide polymorphism) datasets. This R-based implementation of SNP
and genotype filters facilitates
an interactive and iterative SNP filtering pipeline, which can be documented
reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing
various quality and missing data metrics for a SNP dataset, and then filtering
the dataset based on user specified cutoffs.
All functions take 'vcfR' objects as input, which can easily be
generated by reading standard vcf (variant call format) files into R using
the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>).
Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be
written to a local directory in standard vcf format using the 'vcfR' package,
for downstream population genetic and phylogenetic analyses.

Devon DeRaad

SNPfiltR

Interactively Filter SNP Datasets

hard_filter function

<dl><dt>vcfR</dt>
<dd>a vcfR object</dd>
<dt>depth</dt>
<dd>an integer representing the minimum depth for genotype calls that you
wish to retain
(e.g. 'depth = 5' would remove all genotypes with a sequencing depth of 4 reads or less)</dd>
<dt>gq</dt>
<dd>an integer representing the minimum genotype quality for
genotype calls that you wish to retain
(e.g. 'gq = 30' would remove all genotypes with a quality score of 29 or lower)</dd></dl>

Arguments

Hard filter a vcf file by depth and genotype quality (gq) — hard_filter

<dl>

<dt>vcfR</dt>
<dd>a vcfR object</dd>


<dt>depth</dt>
<dd>an integer representing the minimum depth for genotype calls that you
wish to retain
(e.g. 'depth = 5' would remove all genotypes with a sequencing depth of 4 reads or less)</dd>


<dt>gq</dt>
<dd>an integer representing the minimum genotype quality for
genotype calls that you wish to retain
(e.g. 'gq = 30' would remove all genotypes with a quality score of 29 or lower)</dd>

</dl>

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hard_filter: Hard filter a vcf file by depth and genotype quality (gq)

Description

Usage

Value

Arguments

Examples