Tools to work with variant call format files
v1.15.0
Released on CRAN 2022-07-16
vcfR2hapmap()
to convert data for use in GAPITReleased on CRAN 2020-06-05
Released on CRAN 2020-02-06
Released on CRAN 2020-01-10
GPL
to GPL-3
(#144).extract.haps()
reports the correct number of variants processed when verbose.vcfR2loci()
now has the option return.alleles = FALSE
.vcfR2genind()
now has the option retrun.alleles = FALSE
.extract.haps()
did not include the parameter return.alleles = TRUE
in it's call to extract.gt()
in the haploid branch of the function. This parameter has now been added. This also affects vcfR2DNAbin()
which calls this function.vcfR2genlight()
includes the parameter ...
to pass parameters to adegenet::df2genind()
.is.indel()
returns logical vector to identify indels.Released on CRAN 2018-04-17
.vcf_stats_gz()
reports number of elements in header as well as the file's last line. This is used by read.vcfR()
to check for poorly formed files.show
method for vcfR now queries @fix instead of @gt.check_keys()
checks key definitions in the meta section to make sure they are unique.freq_peak_plot()
has parameter posUnits
to adjust units of scatterplot.vcfR2migrate()
manual discusses Unix and Windows line endings.This version was released to coincide with the submission of a manuscript on the subject of the inference of copy number variation.
Released on CRAN 2018-02-07.
vcf_field_names()
now delimts on KEY= of key/value pairs, allows commas to be used within value.read.vcfR()
will download files when provided with a link.data(vep)
.Released on CRAN 2017-12-08.
vcfR2DNAbin()
can include indels and maintains alignment.write.vcf()
now handles tilde expansion.rePOS()
attempts to create a non-overlapping coordinate system from POS and CHROM.vcfR2DNAbin()
manages the asterisk allele.extract.indels()
ignores GATK's <NON_REF>.proc.chromR()
.peak_to_ploid()
to call peaks and calculate dfe from freq_peak()
output.freq_peak_plot()
to help visualize the output of freq_peak()
..vcf_stats_gz
now has nrows and skip parameters..Call()
statements to standardize style.vcfR2migrate()
to output MigrateN format data.freq_peak()
.pairwise_genetic_diff()
to calculate pairwise differentiation.Released on CRAN 2017-05-18.
genetic_diff()
to calculate fixation indicies.pinfsc50.png
to tools.samples
parameter to vcfR method [
.length()
method for chromR objects.[
method throws warning if FORMAT is omitted.plot()
for signature 'chromR' handles INFO column when its all NA.create.chrom()
subsets to first chromosome when more than one is provided.