vcf2genoClasses | R Documentation |
Convert genotypes at SNPs from a VCF file into genotypic classes.
vcf2genoClasses(
vcf.file,
genome = "",
gclasses.file,
ca.file,
yieldSize = NA_integer_,
dict.file = NULL,
seq.id = NULL,
seq.start = NULL,
seq.end = NULL,
na.string = NA,
single.alt = TRUE,
verbose = 1
)
vcf.file |
path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created) |
genome |
genome identifier (e.g. "VITVI_12x2") |
gclasses.file |
path to the output file to record genotypes into genotypic classes (will be gzipped if suffix is ".gz") |
ca.file |
path to the output file to record SNP 1-based coordinates and alleles (will be gzipped if suffix is ".gz") |
yieldSize |
number of records to yield each time the file is read from (see |
dict.file |
path to the SAM dict file (see https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary) if seq.id is specified with no start/end |
seq.id |
see |
seq.start |
see |
seq.end |
see |
na.string |
a symbol to indicate missing genotypes (e.g. NA, "NN", "–", etc) |
single.alt |
if TRUE, only records with a single 'alt' are kept |
verbose |
verbosity level (0/1) |
invisible vector with the path to the output file
Gautier Sarah, Timothee Flutre
gtVcf2genoClasses
, filterVariantCalls
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