Preparing the Inputs

CharGer relies on the annotations in the input VCF, and additional annotations for different classification rules/modules. This page helps the user to prepare all the inputs for CharGer.

Input variants

Note

The resulting file goes to --input command line option or CharGerConfig.input.

Normalize the variants

bcftools norm \
    -f /path/to/genome_ref.fa
    --multiallelics - \
    --check-ref e \
    -Oz -o input_normalized.vcf.gz \
    input.vcf.gz

Annotate the variants using Ensembl VEP

vep --format vcf --vcf \
    --assembly GRCh38 \
    --everything --af_exac \
    --offline \
    --cache --dir_cache /path/to/vep_cache/ \
    --fasta /path/to/Homo_sapiens.GRCh38.dna.toplevel.fa \
    --input_file input_normalized.vcf.gz \
    --output_file input_normalized.vep.vcf

Known pathogenic variants

Note

The resulting file goes to --pathogenic-variant command line option or CharGerConfig.pathognic_variant.

Inheritance gene table

Note

The resulting file goes to --inheritance-gene-table command line option or CharGerConfig.inheritance_gene_table.

HotSpot3D results

Note

The resulting file goes to --hotspot3d-cluster command line option or CharGerConfig.hotspot3d_cluster.