Support VCF - discussion thread - Githubissues

oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.

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Support VCF - discussion thread #197

Open zhx828 opened 1 year ago

zhx828 commented 1 year ago

We have received some interests to annotate VCF file directly in oncokb-annotator. The following items need to be address to support the feature.

Background info

I learned about VCF through this series https://www.youtube.com/watch?v=xHPm0DKAS7c from LiquidBrain Bioinformatics
VCF/BAM format definitions: http://samtools.github.io/hts-specs/
MAF format definitions: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/
README from vcf2maf https://raw.githubusercontent.com/mskcc/vcf2maf/main/docs/vep_maf_readme.txt

### To-do items(not complete list)
- [ ] Understand vcf2maf, particularly look into whether QUAL/FILTER columns from VCF would need input from users. What's the default  
- [ ] Figure out how long it's gonna take to annotate one variant through vcf2maf(do 100 variants and do an average?)
- [ ]

zhx828 commented 1 year ago

GenomeNexus produced an annotation-tools for GENIE which is used to merge VCF and MAF files. We can consider using it to annotate VCF.