Hit enter too quickly: yes, each of the annotations will be in a separate column. For example:
##INFO=<ID=MyFeature1,Number=1,Type=STRING,Description="PF3D7_0100100"> ##INFO=<ID=MyFeature2,Number=1,Type=STRING,Description="PF3D7_0100100"> annots.tab: CHROM POS MyFeature1 MyFeature2 1 1 SomeText1 SomeText2 and the INFO column of the VCF will be annotated like this: MyFeature1=SomeText1;MyFeature2=SomeText2 Petr On Fri, 2015-11-06 at 15:48 +0100, Petr Danecek wrote: > Your header should look like this: > > ##INFO=<ID=MyFeature,Number=1,Type=STRING,Description="PF3D7_0100100"> > > rather than this: > > ##FEATURE=<ID=STRING_TAG,Number=1,Type=STRING,Description="PF3D7_0100100"> > > After the annotation is added, it will appear in the INFO column as > MyFeature=SomeString > > Petr > > > On Fri, 2015-11-06 at 14:45 +0000, Tagliamonte,Massimiliano S wrote: > > Thank you for the follow up, I'm still learning my way through the SNP > > analysis. > > > > I checked again the vcf specifications and the bcftools annotate > > instruction. At this point I am not sure I understand: does each tag > > (i.e. WebId, LocusTag, etc) need to be in a different column of my > > tab-delimited file? > > > Regards, > > Max > > > > Massimiliano S. Tagliamonte > > Graduate Student > > University of Florida > > College of Veterinary Medicine > > Department of Infectious Diseases and Pathology > > > > ________________________________________ > > From: Petr Danecek <[email protected]> > > Sent: Friday, November 6, 2015 5:35 AM > > To: Tagliamonte,Massimiliano S > > Cc: John Marshall; [email protected] > > Subject: Re: [Samtools-help] bcftools annotate could not parse header line > > > > 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 > > > > > > -- > > > 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. > > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > > > Samtools-help mailing list > > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > > > > > > > -- > > 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. > -- 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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
