Hi, the merging does not know how to treat these fields - what type they are and how many fields to expect. You'll have to fix the headers, see `bcftools reheader`
Petr On Tue, 2015-12-22 at 16:38 +0000, Guertin, Michael J. (mjg7y) wrote: > Dear bcftools list, > > > I downloaded TCGA *birdseed.txt files, converted to vcf using > "https://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/contest/BirdseedToVCF.py”, > separated by chromosomes, sorted, zipped and indexed the files. > > > the command: > > > bcftools merge $(ls -1 chr1_*.vcf.gz) > TCGA_chr1_merged.vcf.gz > > > brings up the error: > [W::vcf_parse] INFO 'PID' is not defined in the header, assuming > Type=String > [W::_vcf_parse_format] FORMAT 'GT' is not defined in the header, > assuming Type=String > [W::_vcf_parse_format] FORMAT 'DP' is not defined in the header, > assuming Type=String > [W::_vcf_parse_format] FORMAT 'GQ' is not defined in the header, > assuming Type=String > Error: The INFO field is not defined in the header: PID > > > I do not get this error when merging with vcf-merge, but I want to > incorporate bcftools into the pipeline. > I include an example of the header below—thanks in advance for > suggestions. I do realize that the INFO field is not defined in the > header, but this field does not carry over when converting from > birdseed, neither do the other fields. > > > ##fileformat=VCFv4.1 > ##CreatedBy=BirdseedToVCF-v1.1 > ##CreatedOn=2015-12-20:14:06 > #CHROMPOS IDREF ALTQUAL FILTERINFO FORMATTCGA-sample > chr11156131 rs2887286T C60 .PID=SNP_A-2131660 GT:DP:GQ 0/0:0:60 > chr12234251 rs1496555A G60 .PID=SNP_A-1967418 GT:DP:GQ 0/1:0:60 > ------------------------------------------------------------------------------ > _______________________________________________ > 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. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
