Process paired tumor-normal VCF variants annotated with SnpEff for neoantigen prediction using
garnish_variants(vcfs, tumor_sample_name = "TUMOR")
Paths to one or more VFC files to import. See details below.
Character, name of column in vcf of tumor sample, used to determine mutant allelic fraction of neoantigens.
A data table with one unique SnpEff variant annotation per row, including:
sample_id: sample identifier constructed from input
.vcf file names
se: SnpEff annotation
effect_type: SnpEff effect type
ensembl_transcript_id: transcript effected
ensembl_gene_id: gene effected
protein_change: protein change in HGVS format
cDNA_change: cDNA change in HGVS format
protein_coding: is the variant protein coding?
if CF or AF fields in provided in input VCFs, either:
cellular_fraction: cell fraction taken from input, such as from clonality estimates from PureCN
allelic_fraction: allelic fraction taken from input
vcfs must be annotated with SnpEff.
vcfs can optionally contain an
CF INFO field, in which case cellular fraction or allelic fraction is considered when ranking neoantigens. See example vcf. Single samples are required. Multi-sample
vcfs are not supported.
Variant filtering according to experimental specifications.
Classification by somatic status and clonality using PureCN.
Annotate variants using SnpEff (required).
Krøigård AB, Thomassen M, Lænkholm A-V, Kruse TA, Larsen MJ. 2016. Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data. PLoS ONE. 11(3):e0151664
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, et al. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 6(2):80–92
Riester M, Singh AP, Brannon AR, Yu K, Campbell CD, et al. 2016. PureCN: copy number calling and SNV classification using targeted short read sequencing. Source Code Biol Med. 11(1):13
Callari M, Sammut SJ, De Mattos-Arruda L, Bruna A, Rueda OM, Chin SF, and Caldas C. 2017. Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Medicine. 9:35.