dart2vcf: Convert DArTag to VCF
| dart2vcf | R Documentation |
Convert DArTag to VCF
Description
Convert DArTag to VCF
Usage
dart2vcf(counts.file, dosage.file, vcf.file, ploidy, first.data.row = 9)
Arguments
counts.file |
DArTag collapsed counts file |
dosage.file |
DArTag dosage file |
vcf.file |
name of VCF output file |
ploidy |
ploidy |
first.data.row |
default is 9 for DArTag format |
Details
Two input files expected. counts.file is the two-row collapsed counts file, whereas dosage.file has one row per target, with chrom and position in columns 4 and 5. DArT reports dosage of REF, whereas VCF standard is based on dosage of ALT. The dosage is exported as GT field in VCF.
Duplicate samples are renamed by appending the "Target ID".
