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
