Support VCF - discussion thread

[zhx828]

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

Tasks

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1. Understand vcf2maf, particularly look into whether QUAL/FILTER columns from VCF would need input from users. What's the default
2. Figure out how long it's gonna take to annotate one variant through vcf2maf(do 100 variants and do an average?)

[zhx828]

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