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

[Heng Li <lh...@sa...>]

I agree that we should mandate TAB as the field separator. The parser should reject a VCF using space as the separator. I am also inclined to disallow space in INFO, though not strongly. Using underlines seems a better solution to me. If the purpose of detailed functional annotations is for human to read, underlines look better than spaces as you will not confuse an underline with a TAB.

Heng

On Nov 26, 2012, at 7:52 AM, Petr Danecek wrote:

> 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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-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.