filter.vcf: Filter a VCF file or vcfR object. Filter or sample...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

Filter a VCF file or vcfR object. Filter or sample individuals or sites of a SNPs dataset held in either a VCF file or vcfR object. Possible filtering criteria include missingness, site variation, homozygosity (not yet implemented), and the function provides three simple methods for obtaining "unlinked" SNPs. Includes options for changing some aspects of formatting, but still within withi the VCF specifications. The function depends on the vcfR. for reading and writing VCF files into R are from the package vcfR. NOT QUITE FUNCTIONAL.

Description

Filter a VCF file or vcfR object.

Filter or sample individuals or sites of a SNPs dataset held in either a VCF file or vcfR object. Possible filtering criteria include missingness, site variation, homozygosity (not yet implemented), and the function provides three simple methods for obtaining "unlinked" SNPs. Includes options for changing some aspects of formatting, but still within withi the VCF specifications. The function depends on the vcfR. for reading and writing VCF files into R are from the package vcfR. NOT QUITE FUNCTIONAL.

Usage

filter.vcf(
  x,
  save.as = NULL,
  nsample = c(NA, NA),
  specificSites = NULL,
  specificIndv = NULL,
  only.GT = TRUE,
  sep.GT = "/",
  min.n = 4,
  min.n0 = 2,
  min.n1 = 1,
  method.linked = "best",
  no.indv = FALSE
)

Arguments

x	Either a vcfR object or a character string to the input VCF file.
save.as	Null or a character string where output VCF should be saved.
nsample	A vector with two values, each NA or a number, specifying the number of individuals and sites, respectively, to randomly retain after applying the other filtering rules. Default value c(NA,NA) retains all individuals and sites that pass other filtering criteria.
specificSites	Numerical vector with which sites to keep or to sample within. Default NULL.
specificIndv	Character string with names of individuals to keep or to sample within. Default is NULL (all individuals kept).
only.GT	Logical indicating whether or not extra, non-genotype information should be included in the genotype columns of the output VCF. Default FALSE. If TRUE, all entries of the 'FORMAT' column will be 'GT', and the genotype columns will only include genotype data.
sep.GT	Character string with the separator to use for haplotypes if individuals are polyploid. Default "/", but "|" is also valid. No other separators valid.
min.n	Minimum number of non-missing alleles required to keep a site. Default = 4. If set to "all", then no sites with any missing data are removed (after first filtering individuals if indv.keep is non-NULL).
min.n0	Minimum number of individuals required to have at least one copy of the major allele to keep a site. Default = 2.
min.n1	Minimum number of individuals required to have at least one copy of the minor allele to keep a site. Default = 1.
method.linked	Character string indicating the method for choosing a site to keep for each locus (or chromosome). Default = "best", which is considered the one with the least missing data, or the first among sites tied for least missing data. Other options are "all.passing", which retains all sites (positions) that pass variation filters (min.n, min.0.n.0, min.1.n), "first" (first site kept at each locus), or "random".
no.indv	Logical. If TRUE, specifies that the VCF does not include genotype information for specific individuals. Default FALSE. If there are no individuals and this is left FALSE then an error will be generated.

Value

A vcfR object

Examples

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium_AllSpecies_AllSNPs.vcf",out="Oxyrhabdium_AllSpecies_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium-modestum_AllSNPs.vcf",out="Oxyrhabdium-modestum_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium-cf.modestum_AllSNPs.vcf",out="Oxyrhabdium-cf.modestum_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium-cf.modestum_Luzon_AllSNPs.vcf",out="Oxyrhabdium-cf.modestum_Luzon_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium-leporinum_AllSNPs.vcf",out="Oxyrhabdium-leporinum_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium-leporinum_Luzon_AllSNPs.vcf",out="Oxyrhabdium-leporinum_Luzon_BestSNP.vcf")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium_both-modestum_AllSNPs.vcf",out="Oxyrhabdium_both-modestum_AllSNPs.vcf",which.site="all.passing")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium_both-modestum_AllSNPs.vcf",out="Oxyrhabdium_both-modestum_BestSNP.vcf",which.site="best")

vcf_getSNP(vcftools.path="/vcftools",vcf="Oxyrhabdium_AllSpecies_AllSNPs.vcf", indv.keep="indv_keep_Oxyrhabdium_both-modestum.txt", out="Oxyrhabdium_both-modestum_BestSNP.vcf", which.site="best")

vcf_getSNP(vcftools.path="/panfs/pfs.local/home/j926w878/programs/vcftools_0.1.13/bin/vcftools",vcf="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/Ahaetulla_snps.vcf",indv.keep="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/indv_keep_Ahaetulla-prasina_AllLocalities_GoodData.txt",out="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_AllPops_AllSNPs.vcf",which.site="all.passing")

vcf_getSNP(vcftools.path="/panfs/pfs.local/home/j926w878/programs/vcftools_0.1.13/bin/vcftools",vcf="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/Ahaetulla_snps.vcf",indv.keep="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/indv_keep_Ahaetulla-prasina_AllLocalities_GoodData.txt",out="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_AllPops_FirstSNP.vcf",which.site="first")

vcf_getSNP(vcftools.path="/panfs/pfs.local/home/j926w878/programs/vcftools_0.1.13/bin/vcftools",vcf="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_AllPops_AllSNPs.vcf",indv.keep="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/indv_keep_Ahaetulla-prasina_Luzon.txt",out="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_Luzon_BestSNP.vcf",which.site="best")

vcf_getSNP(vcftools.path="/panfs/pfs.local/home/j926w878/programs/vcftools_0.1.13/bin/vcftools",vcf="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_AllPops_AllSNPs.vcf",indv.keep="/panfs/pfs.local/home/j926w878/programs/easySFS/popfiles/indv_keep_Ahaetulla-prasina_Luzon.txt",out="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Ahaetulla-prasina_Luzon_NoMissingData.vcf",which.site="all.passing",min.n = (19*2))

vcf_getSNP(vcftools.path="/panfs/pfs.local/home/j926w878/programs/vcftools_0.1.13/bin/vcftools",vcf="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Calamaria-gervaisii_AllPops_AllSNPs.vcf",indv.keep=NULL,out="/panfs/pfs.local/home/j926w878/work/ddRAD/snps_goodData/Calamaria-gervaisii_AllPops_BestSNP.vcf",which.site="best")

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.