Parse ANN field

[cmdcolin]

The ANN field is something with fields defined in the header and the field is | delimited https://github.com/GMOD/vcf-js/tree/add_ann_example

There is also SVANN I think

[cmdcolin]

It doesn't look like tools are being helpful in standardizing the field representation

The header line in the jannovar example is

##INFO=<ID=ANN,Number=1,Type=String,Description="Functional annotations:'Allele|Annotation|Annotation_Impact|Gene_Name|Gene_ID|Feature_Type|Feature_ID|Transcript_BioType|Rank|HGVS.c|HGVS.p|cDNA.pos / cDNA.length|CDS.pos / CDS.length|AA.pos / AA.length|Distance|ERRORS / WARNINGS / INFO'">

Am I to assume that "Functional annotations: " is not just some freetext and is something I can programmatically parse?

SnpEff proposes some standard layout of the ANN field but that might not be actually standard http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf (haven't seen the header of the snpeff vcf but they might not include their version of it in the header info)

[garrettjstevens]

I'm pretty sure Jannovar uses the same standard as SnpEff. I thought I saw that somewhere, but now I can't remember where. The history seems to imply they started using that in v0.12, though: https://doc-openbio.readthedocs.io/projects/jannovar/en/master/history.html

[cmdcolin]

There is also EFF but that is outdated "Note: Older SnpEff version used 'EFF' field (details about the 'EFF' field format can be found in the EFF Field section)."

[cmdcolin]

There is also CSQ from VEP https://useast.ensembl.org/info/docs/tools/vep/vep_formats.html

this is sort of interesting from the GSoC projects on VEP

[cmdcolin]

probably code done on consuming app