mkClinvarTxt: Download ClinVar vcf and convert to txt file
In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output
Description
Download ClinVar vcf and convert to txt file
Usage
1
2
3
4
5
6
7
8
mkClinvarTxt(
out.file,
tmp.dir = "~/",
url = "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20200224.vcf.gz",
java.path = JAVA_PATH,
snpsift.path = SNPSIFT_PATH,
verbose = T
)
Arguments
out.file
Path to output file
tmp.dir
Temporary processing directory. Defaults to ~/
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)
verbose
Show progress messages?
luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.
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.
Description
Download ClinVar vcf and convert to txt file
Usage
1 2 3 4 5 6 7 8 | mkClinvarTxt(
out.file,
tmp.dir = "~/",
url = "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20200224.vcf.gz",
java.path = JAVA_PATH,
snpsift.path = SNPSIFT_PATH,
verbose = T
)
|
Arguments
out.file |
Path to output file |
tmp.dir |
Temporary processing directory. Defaults to ~/ |
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) |
verbose |
Show progress messages? |
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.