This directory includes HG002Trio.vcf.gz, a small subset of variant calls for the HG002/HG003/HG004 trio plus 20 unrelated samples used by novoCaller. Variants are fully annotated with VEP, and both novoCaller and comHet were run to refine calls for HG002.

This file is intended as a lightweight test dataset for:

• the granite VCF parser (granite.lib.vcf_parser)
• the filtering utilities (e.g. filterByTag)

This example extracts variants where the child is not homozygous reference (0/0) and both parents are homozygous reference (0/0).

from granite.lib import vcf_parser

# Samples to extract variants for
child = "NA24385_sample"
father = "NA24149_sample"
mother = "NA24143_sample"

# Load the VCF file
vcf_obj = vcf_parser.Vcf("HG002Trio.vcf.gz")

# Open output file and write the header
with open("HG002Trio_test_parser.vcf", "w") as fo:
    vcf_obj.write_header(fo)

    # Iterate through variants
    for vnt_obj in vcf_obj.parse_variants():

        # Extract genotype (GT) values
        GT_child = vnt_obj.get_genotype_value(child, "GT")
        GT_father = vnt_obj.get_genotype_value(father, "GT")
        GT_mother = vnt_obj.get_genotype_value(mother, "GT")

        # Child is non-reference; both parents are homozygous reference
        if GT_child not in ("0/0", "0|0") and GT_father in ("0/0", "0|0") and GT_mother in ("0/0", "0|0"):
            vcf_obj.write_variant(fo, vnt_obj)

Note:
The condition above selects variants where the child carries at least one alternate allele (heterozygous or homozygous alternate). If you want to restrict to only homozygous alternate calls, explicitly check for 1/1 or 1|1.

Extract variants with novoPP >= 0.9:

granite filterByTag \
  -i HG002Trio.vcf.gz \
  -o HG002Trio_test_filter.vcf \
  -t 'novoPP/0.9/>=/float/any'

Extract variants with novoPP >= 0.9 and annotated as missense_variant in the VEP Consequence field:

granite filterByTag \
  -i HG002Trio.vcf.gz \
  -o HG002Trio_test_filter.vcf \
  -t 'novoPP/0.9/>=/float/any' \
     'Consequence/missense_variant/~/str/any/field=|/entry=,/value=&' \
  --logic all

Notes:

• The ~ operator is used to match substrings, which is required for VEP Consequence values such as
  missense_variant&splice_region_variant.
• field=| specifies the VEP field separator.
• entry=, specifies the separator between multiple transcript annotations.
• value=& specifies the separator for multiple consequence terms within a transcript.
• All string matching is case-sensitive.