setGt2Na | R Documentation |
Set genotypes (GT field) to missing if the genotype quality (GQ field) isn't high enough.
setGt2Na(
vcf.file,
genome = "",
out.file,
yieldSize = NA_integer_,
dict.file = NULL,
seq.id = NULL,
seq.start = NULL,
seq.end = NULL,
min.gq = 90,
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") |
out.file |
path to the output VCF file (a bgzip index will be created in the same directory) |
yieldSize |
number of records to yield each time the file is read from (see ?TabixFile) if seq.id is NULL |
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 |
sequence identifier to work on (e.g. "chr2") |
seq.start |
start of the sequence to work on (if NULL, whole seq) |
seq.end |
end of the sequence to work on (if NULL, whole seq) |
min.gq |
minimum GQ below which GT is set to missing |
verbose |
verbosity level (0/1) |
the destination file path as an invisible character(1)
Timothee Flutre
filterVariantCalls
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