readVarDict: Read in input vcf data in VarDict format for Contamination...
In vanquish: Variant Quality Investigation Helper
Description
Usage
Arguments
Value
Description
Read in input vcf data in VarDict format for Contamination detection
Usage
1
readVarDict(dr, dbOnly, depCut, thred, content, extnum, keepall)
Arguments
dr
A valid input object
dbOnly
Use dbSNP as filter, default is FALSE, passed from read_vcf
depCut
Use a threshold for min depth , default is False
thred
Threshold for min depth, default is 20
content
Column names in VCF files
extnum
The column number to be extracted from vcf, default is 10; 0 for not extracting any column
keepall
Keep unextracted column in output, default is TRUE, passed from read_vcf
Value
Dataframe from VCF file
vanquish documentation built on May 2, 2019, 9:42 a.m.
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Description Usage Arguments Value
Description
Read in input vcf data in VarDict format for Contamination detection
Usage
1 | readVarDict(dr, dbOnly, depCut, thred, content, extnum, keepall)
|
Arguments
dr |
A valid input object |
dbOnly |
Use dbSNP as filter, default is FALSE, passed from read_vcf |
depCut |
Use a threshold for min depth , default is False |
thred |
Threshold for min depth, default is 20 |
content |
Column names in VCF files |
extnum |
The column number to be extracted from vcf, default is 10; 0 for not extracting any column |
keepall |
Keep unextracted column in output, default is TRUE, passed from read_vcf |
Value
Dataframe from VCF 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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