It is an R package to make a pseudo reference genome subsituted with the SNP variants of given samples.
Install devtools first, and then use devtools to install pseudoRef from github.
devtools::install_github("yangjl/pseudoRef")
It requires two other papckages:
library("data.table")
library("Biostrings")
You can find help documentation by simply typing ?pseudoRef, which is the major function have been implemented in this package.
Usage:
pseudoRef(fa, snpdt, sidx = 5:ncol(snpdt), arules = NULL, outdir)
Arguments:
fa: Path for the reference fasta file. [string or
DNAStringSet/DNAString object]
snpdt: A data.table object with heterozygote SNPs coded with IUPAC
ambiguity codes. [data.table, 4 required columns: chr, pos,
ref, alt, (sample1, ..., sampleN)]
sidx: A vector to indicate the sample columns. [vector,
default=5:ncol(snpdt)].
arules: Additional nucleotide substitution rules defined by users.
[data.frame, 2 required columns: from, to, default=NULL] For
example, arules <- data.frame(from=c("M", "Y", "R", "K"),
to=c("C", "C", "G", "T")).
outdir: Output directory. Sample specific sub-folders will be
created. [string]
Before running the package, we should use BCFtools to convert VCF/BCF file into IUPAC coded tab seperated file:
# bcftools view JRI20_filtered_snps_annot.bcf.gz -m2 -M2 -v snps -Oz -o JRI20_bi_snps_annot.vcf.gz
# bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%IUPACGT]\n' JRI20_bi_snps_annot.vcf.gz > JRI20_bi_snps_annot.txt
# bcftools query -f 'chr\tpos\tref\talt[\t%SAMPLE]\n' JRI20_bi_snps_annot.vcf.gz > JRI20_bi_snps_annot.header
This package is free and open source software, licensed under GPL.