Re: [Samtools-help] bcftools annotate could not parse header line

[Tagliamonte,Massimiliano S <mst...@uf...>]

Great, I'll replace the underscores then.

Thanks for your help,
Max

Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology

________________________________________
From: John Marshall <jm...@sa...>
Sent: Thursday, November 5, 2015 6:47 AM
To: Tagliamonte,Massimiliano S
Cc: sam...@li...
Subject: Re: [Samtools-help] bcftools annotate could not parse header line

On 4 Nov 2015, at 21:25, Tagliamonte,Massimiliano S <mst...@uf...> wrote:
> I am trying to add an annotation column to my vcf file, after calling variants with the Samtools 1.x pipeline. I am using bcftools annotate, but I keep getting the same error regarding one of the headers:
> Could not parse the header line: "##FEATURE=<web_id=STRING_TAG,Number=1,Type=STRING,Description="PF3D7_0100100">"

It's complaining about the underscore in your "web_id" key.  Prior to VCF v4.3, the spec gave no hints about what characters might be in INFO et al field keys [1], and somewhat unfortunately htslib/bcftools allowed for only letters and digits.  This has been relaxed on the develop branch in GitHub [2] and underscores and (non-leading) dots will be accepted by the next bcftools release.

In the meantime, you could either build htslib and bcftools from the development branches in their GitHub repositories, or remove the underscores from your web_id and locus_tag to get this to work with bcftools 1.2.

    John

[1] In the v4.3 spec, see §1.6.1/8
[2] https://github.com/samtools/htslib/commit/30fb9eee41953958923c56f7ea0af5a5b0376b94

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