VCF Genotype Annotator¶
The VCF Genotype Annotator will take an existing VCF file and add a new sample
to it. The sample name is set via the second positional argument.
The sample’s GT field is pre-populated with a default value given by
the third positional argument. Options are 0/1
, 1/1
, 0/0
, or
.
.
It can also be used to add a GT field to an existing sample, e.g. for VCFs created by Strelka which does not output a GT field for its calls.
By default the output VCF will be written to a .genotype.vcf
file next to
your input VCF file. You can set a different output file using the
--output-vcf
parameter.
Usage¶
usage: vcf-genotype-annotator [-h] [-o OUTPUT_VCF]
input_vcf sample_name {0/1,1/1,0/0,.}
A tool to add a new sample to an existing VCF file or fill in the GT field for
an existing sample in a VCF.
positional arguments:
input_vcf A VCF file
sample_name The name of the sample to add
{0/1,1/1,0/0,.} The genotype value to add to the GT field
optional arguments:
-h, --help show this help message and exit
-o OUTPUT_VCF, --output-vcf OUTPUT_VCF
Path to write the output VCF file. If not provided,
the output VCF file will be written next to the input
VCF file with a .genotype.vcf file ending.