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 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TCGA-sample chr1 1156131 rs2887286 T C 60 . PID=SNP_A-2131660 GT:DP:GQ 0/0:0:60 chr1 2234251 rs1496555 A G 60 . PID=SNP_A-1967418 GT:DP:GQ 0/1:0:60
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