Description Usage Arguments Value
View source: R/preProcessSnvIndel.R
Annotate variant type with snpEff
1 2 3 4 5 6 7 | annotateVariantType(
vcf.file,
out.file,
genome = "GRCh37.75",
java.path = JAVA_PATH,
snpeff.path = SNPEFF_PATH
)
|
vcf.file |
Path to vcf file (gzip compressed) |
out.file |
Path to output txt file (make sure to add .gz at the end) |
genome |
Name of the genome to supply to snpEff |
java.path |
Path to java binary (defaults to the installed JRE location) |
snpsift.path |
Path to SnpSift jar (defaults to the one included in this package) |
Nothing but writes a gzipped txt file
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