readVarDict function

Read in input vcf data in VarDict format for Contamination detection

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

Returns

Dataframe from VCF file