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: 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.