Adding genotype sample information to your VCF¶
pVACseq was primarily designed for clinical application. As such, it requires
that the input VCF contains sample genotype information (
GT field), which identifies
whether or not a variant was called in a specific sample of interest.
Some variant callers (e.g., Strelka), however, do not include this field. In
other use cases you might want to run pVACseq on a list of variants of interest. If your
input VCF does not contain sample information (i.e. no
and/or sample column) or the
FORMAT list does not contain a
you will need to preprocess your VCF to add this information.
This information can be added using the VAtools
Using the vcf-genotype-annotator to add genotype information to your VCF¶
Installing the vcf-genotype-annotator¶
vcf-genotype-annotator is part of the
Please visit vatools.org for more details on this package.
You can install this package by running:
pip install vatools
Running the vcf-genotype-annotator¶
Example vcf-genotype-annotator commands
vcf-genotype-annotator <input_vcf> <sample_name> 0/1 -o <gt_annotated_vcf>
sample_name argument is used as the sample name in the
of your VCF when adding a new sample with this tool. If you want to add a
field to an existing sample in your VCF, this argument will need to match the name of that sample.
Please see the VAtools documentation for more information.