vcf2dosage | R Documentation |
Convert genotypes at bi-allelic variants from a VCF file into allele doses.
This is also doable with bcftools +dosage
.
vcf2dosage(
vcf.file,
genome = "",
gdose.file,
ca.file,
yieldSize = NA_integer_,
dict.file = NULL,
seq.id = NULL,
seq.start = NULL,
seq.end = NULL,
field = "GT",
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") |
gdose.file |
path to the output file to record genotypes as allele doses (will be gzipped); variants will be in rows and samples in columns |
ca.file |
path to the output file to record SNP 1-based coordinates and alleles (will be gzipped) |
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 |
see |
seq.start |
see |
seq.end |
see |
field |
the genotypes to convert should come from the "GT" or "DS" fields |
verbose |
verbosity level (0/1) |
an invisible list with both output file paths
Timothee Flutre
gtVcf2dose
, dsVcf2dose
, filterVariantCalls
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