Re: [VCFtools-spec] Wishlist for 4.2: allow space characters in INFO; functional annotation

[Petr D. <pd...@sa...>]

Hi Gonzalo,

I welcome the idea of standardizing the functional annotations. Here is
an example of a wildly evolved format that we have been using so far:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence of the ALT
alleles from Ensembl 66 VEP v2.4, format
transcriptId:geneName:consequence[:codingSeqPosition:proteinPosition:proteinAlleles:proteinPredictions]+...[+gerpScore]">

and two concrete examples, the first for a multiallelic site:

CSQ=621:S>R:Grantham,110:Allele,C:Gene,Ssh3
+ENSMUST00000037992:ENSMUSG00000034616:SYNONYMOUS_CODING:1863:621:S>S:Allele,A:Gene,Ssh3

CSQ=ENST00000382410:DEFB125:NON_SYNONYMOUS_CODING:184:62:H>Y:SIFT,tolerated(0.41):PolyPhen,benign(0):Condel,neutral(0.015):Grantham,83

I am curious what other formats are in use?


I'd prefer not to introduce whitespaces in the INFO field or change the
column delimiters to spaces or extend to whitespaces; it would break
existing software and wouldn't bring much benefit.

Petr



On Mon, 2012-11-26 at 11:20 +0000, Peter Cock wrote:
> On Mon, Nov 26, 2012 at 5:12 AM, Eric Banks <eb...@br...> wrote:
> > Hi Bradford,
> >
> > I do understand where you're coming from, but truthfully I'd prefer to go in
> > the opposite direction once we're open to changing delimiters.  I've never
> > quite understood why VCF is tab-delimited and not whitespace-delimited.
> 
> Tab separated makes it easy to use in Galaxy, R, etc, even Excel - please
> keep that. It is a good thing!
> 
> > You wouldn't believe how many times people have manually generated
> > VCFs that were space-delimited and couldn't understand why they were
> > failing in VCF parsers.
> 
> I'd be asking why doesn't your parser give a clearer error message?
> If you've seen people fall over this pothole many times the parser
> concerned should be fixed.
> 
> > I'd much rather that all whitespace be treated equally (as it is
> > visually).  It makes for a much simpler spec.
> 
> The problem with white space is you can't see how many characters
> there are - spaces and tabs are not treated equally visually. What
> would you expect if there were several spaces in a row? If you treat
> it as one separator you prevent using empty cells (I'm thinking in
> terms of generalities here, not just VCF).
> 
> Regards,
> 
> Peter




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