parse_vcf_output: Parse a VCF input to return a data frame with standardised...
In annaquaglieri16/samplepower: Compute sensitivity and false positive rates for a variant call set with repsect to a truth dataset.
View source: R/parse_vcf_output.R
Description
Parse a VCF input to return a data frame with standardised fields across callers to use for caller comparison. It only works with germline calls and for VCF from the following callers: GATK3 MuTect2, VarScan2 and VarDict.
Usage
1
parse_vcf_output(vcf_path, sample_name, caller)
Arguments
vcf_path
path to where the '.vcf' file for one sample is saved.
sample_name
character. Sample name of the current 'vcf' file.
caller
character. One of 'mutect', 'vardict' or 'varscan'.
annaquaglieri16/samplepower documentation built on Nov. 7, 2019, 11:43 p.m.
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View source: R/parse_vcf_output.R
Description
Parse a VCF input to return a data frame with standardised fields across callers to use for caller comparison. It only works with germline calls and for VCF from the following callers: GATK3 MuTect2, VarScan2 and VarDict.
Usage
1 | parse_vcf_output(vcf_path, sample_name, caller)
|
Arguments
vcf_path |
path to where the '.vcf' file for one sample is saved. |
sample_name |
character. Sample name of the current 'vcf' file. |
caller |
character. One of 'mutect', 'vardict' or 'varscan'. |
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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