readGATK {vanquish} | R Documentation |
Read in input vcf data in GATK format for Contamination detection
readGATK(dr, dbOnly, depCut, thred, content, extnum, keepall)
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 or numbers to be extracted from vcf, default is 10; 0 for not extracting any columns |
keepall |
Keep unextracted column in output, default is TRUE, passed from read_vcf |
Dataframe from VCF file