VCF annotation

[serge2016]

Hello! Is it possible to generate an annotated tab-separated file from VCF for future processing with pVAC-Seq? If I understand correctlym your first prototype (immuno) could do it.

[iskandr]

Hey @serge2016,

What fields do you need in the output? I haven't used pVAC-Seq so I'm not sure what it expects.

[serge2016]

Dear @iskandr ,

• chromosome_name
• start
• stop
• reference
• variant
• gene_name
• transcript_name
• amino_acid_change (e.g. P776L)
• ensembl_gene_id
• wildtype_amino_acid_sequence

All this is on their main page: https://github.com/griffithlab/pVAC-Seq

[iskandr]

Huh, it looks like pVAC-Seq expects only single amino acid substitutions. Maybe @jasonwalker80, @malachig, or @jhundal can shed light on how I should represent frameshifts and other multi-residue mutations as inputs to pVAC-Seq.

[jhundal]

Hi @iskandr and @serge2016 The current release of pVAC-Seq supports only single amino acid substitutions, but we do plan to add indel support as well as VCF file input in the upcoming releases. You could track the progress here: https://github.com/griffithlab/pVAC-Seq/issues/33

[iskandr]

@serge2016 I could add a flag for generating a pVACSeq TSV that ignores indels. Would that work for your purposes?

[serge2016]

@iskandr It would be great! Thank you!

[susannasiebert]

@serge2016 @iskandr I'm not sure how much work you want to put into supporting the current pVAC-Seq input format since we are actively working on supporting VCFs. The current deadline for this is June 21st. That release would also support frameshifts and inframe indels.

[iskandr]

Hey @susannasiebert, what's your plan for translating frameshifts?

Also, @serge2016, do you still want me to implement this output format for "legacy" pVACSeq?

[serge2016]

@iskandr, it seems to me that some kind of customizable output would be very useful. If it takes not very much time to implement this, I'd very thankful for such option.