Hi Massimiliano,
your FEATURE tag is defined as neither INFO nor FORMAT tag, please check
the VCF specification
http://samtools.github.io/hts-specs/
Best wishes,
Petr
On Thu, 2015-11-05 at 15:58 +0000, Tagliamonte,Massimiliano S wrote:
> OK, sorry to bother again.
>
> I replaced all the underscores, but now I am getting 'The tag "FEATURE" is
> not defined in my_file.tab.gz'
>
> This is my command:
>
> bcftools annotate -a my_file.tab.gz \
> -c CHROM,FROM,TO,FEATURE \
> -h bcftools_annots.hdr \
> -O v -o ./filtering/my_snps_bcftools_annotated.vcf \
> my_snps.vcf.gz
>
> The tab file has no header, and only 4 columns (chrom name, gene start , gene
> end, annotation ('FEATURE') column. I have checked the instructions on
> http://www.htslib.org/doc/bcftools.html#annotate but I am not sure what I am
> doing wrong. This is the tab file first line:
>
> Pf3D7_01_v3 29510 37126
> ID=PF3D7_0100100;Name=PF3D7_0100100;description=erythrocyte+membrane+protein+1%2C+PfEMP1+%28VAR%29;size=7617;WebId=PF3D7_0100100;LocusTag=PF3D7_0100100;size=7617;Alias=VAR-UPSB1,124505645,MAL1P4.01,VAR,PF3D7_0100100,7670005,PFA0005w
>
> Thanks again for your time and kind attention,
> Max
>
>
> Massimiliano S. Tagliamonte
> Graduate Student
> University of Florida
> College of Veterinary Medicine
> Department of Infectious Diseases and Pathology
>
>
> ________________________________________
> From: Tagliamonte,Massimiliano S
> Sent: Thursday, November 5, 2015 9:50 AM
> To: John Marshall
> Cc: [email protected]
> Subject: Re: [Samtools-help] bcftools annotate could not parse header line
>
> 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 <[email protected]>
> Sent: Thursday, November 5, 2015 6:47 AM
> To: Tagliamonte,Massimiliano S
> Cc: [email protected]
> Subject: Re: [Samtools-help] bcftools annotate could not parse header line
>
> On 4 Nov 2015, at 21:25, Tagliamonte,Massimiliano S <[email protected]>
> 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 ยง1.6.1/8
> [2]
> https://github.com/samtools/htslib/commit/30fb9eee41953958923c56f7ea0af5a5b0376b94
>
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