Vaccine Peptides Report

PATIENT INFO

VCF (somatic variants) path(s) {{ vcf_paths }}
BAM (RNAseq reads) path {{ bam_path }}
MHC alleles {{ mhc_alleles }}
Total number of somatic variants {{ num_total_somatic_variants }}
Somatic variants with predicted coding effects {{ num_somatic_variants_with_predicted_coding_effects }}

VARIANTS

    {% for v in variants %}
  1. Variant {{ v.short_description }}
    Gene name {{ v.gene_name }}
    Top score {{ v.top_score|round(2) }}
    Reads supporting variant allele {{ v.reads_supporting_variant_allele }}
    Reads supporting reference allele {{ v.reads_supporting_reference_allele }}
    Reads supporting other alleles {{ v.reads_supporting_other_alleles }}

    Predicted Effect

    Effect type {{ v.predicted_effect.__class__.__name__ }}
    Transcript name {{ v.predicted_effect.transcript_name }}
    Transcript ID {{ v.predicted_effect.transcript_id }}
    Effect description {{ v.predicted_effect.short_description }}

    Vaccine Peptides for variant: {{ v.short_description }}

      {% for p in v.peptides %}
    1. Amino acid sequence {{ p.aa_before_mutation }}{{ p.aa_mutant }}{{ p.aa_after_mutation }}
      Transcript name {{ v.predicted_effect.transcript_name }}
      Length {{ p.length }}
      Expression score {{ p.expression_score|round(2) }}
      Mutant epitope score {{ p.mutant_epitope_score|round(2) }}
      Reads fully spanning cDNA sequence(s) {{ p.num_alt_reads_supporting_protein_sequence }}
      Mutant amino acids {{ p.num_mutant_amino_acids }}
      Mutation distance from edge {{ p.mutation_distance_from_edge }}
      Predicted mutant epitopes {% for e in p.epitopes %} {% endfor %}
      Sequence IC50 Allele
      {{ e.sequence }} {{ e.ic50|round(2) }} {{ e.allele }}
      2. {% endfor %}
    2. {% endfor %}