Welcome to VCFstat Package’s documentation!

VCFstat Package

Author

Michael Hall

Date

4/19/2022

VCFstat Package in R

VCFstat is an R package for Downstream analysis of VCF files.

VCFstat Package is still under development and is offered with out any guarantee.

Build Install and Restart

_images/R_CMD_INSTALL.png

Build R CMD check results

_images/R_CMD_Check_Results.png

Installation

You can install VCFstat from github with:

Note: QTLseqr is a dependent package so

Examples:

Load/install libraries

devtools::install_github("PBGLMichaelHall/VCFstat",force = TRUE)
library(VCFstat)
library(vcfR)
library(data.table)
library(QTLseqr)
library(ggplot2)


# Check to see if all dependent packages are loaded.
sessionInfo()

Example 1 Rice

setwd("/home/michael/Desktop/QTLseqr/extdata/")

chromlist <- c("Chr01","Chr02","Chr03","Chr04","Chr05","Chr06","Chr07","Chr08","Chr09","Chr10")

Functions

VCFstat::ChromQual(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)

VCFstat::ChromDP(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)
_images/2.png 
VCFstat::ChromRO(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)

VCFstat::ChromAO(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)
_images/4.png 
VCFstat::ChromMQM(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)
_images/5.png 
VCFstat::ChromAC(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)

VCFstat::ChromAN(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)

VCFstat::ChromnSNPs(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05)

VCFstat::FacetChromnSNPs(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05, ncol=10)
_images/9.png 
VCFstat::FacetChromQual(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05, ncol=10)

VCFstat::FacetChromDP(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05, ncol=10)

VCFstat::FacetChromAO(vcf = "freebayes_D2.filtered.vcf.gz", chromlist = chromlist,windowSize = 1e+05, ncol=10)
_images/13.png

Example 2 Brachypodium

setwd("/home/michael/Desktop/Variants/Decompressed/")

chromlist <- c("NC_016131.3","NC_016132.3","NC_016133.3","NC_016134.3","NC_016135.3")

Functions

VCFstat::ChromDP(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05)

VCFstat::ChromRO(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::ChromAO(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::ChromMQM(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::ChromAC(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::ChromAN(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::ChromnSNPs(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, binwidth = 10)

VCFstat::FacetChromnSNPs(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, ncol=10)

VCFstat::FacetChromQual(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, ncol=10)

VCFstat::FacetChromDP(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, ncol=10)

VCFstat::FacetChromAO(vcf = "freebayes~bwa~GCF_000005505.3_Brachypodium_distachyon_v3.0~all_samples~filtered-strict.vcf", chromlist = chromlist,windowSize = 1e+05, ncol=10)
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