While technically not a Galaxy (Dev) question, but I am running into a non-standard VCF header in the GATK UnifiedGenotyper output.
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Where Number=G and Number=A which does not pass the VCF Validator filter...
Anyone know what is going on here? I had to change it to actual numbers (as the format describes..)
Where does this header come from in the first place? Is it some standard header?
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