annotateVariantType: Annotate variant type with snpEff
In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output
Description
Usage
Arguments
Value
View source: R/preProcessSnvIndel.R
Description
Annotate variant type with snpEff
Usage
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annotateVariantType(
vcf.file,
out.file,
genome = "GRCh37.75",
java.path = JAVA_PATH,
snpeff.path = SNPEFF_PATH
)
Arguments
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)
Value
Nothing but writes a gzipped txt file
luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.
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Description Usage Arguments Value
View source: R/preProcessSnvIndel.R
Description
Annotate variant type with snpEff
Usage
1 2 3 4 5 6 7 | annotateVariantType(
vcf.file,
out.file,
genome = "GRCh37.75",
java.path = JAVA_PATH,
snpeff.path = SNPEFF_PATH
)
|
Arguments
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) |
Value
Nothing but writes a gzipped txt file
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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