Hi,

I have downloaded Geuvadis genotypes from:

https://www.ebi.ac.uk/arrayexpress/files/E-GEUV-1/GEUVADIS.chr22.PH1PH2_465.IMPFRQFILT_BIALLELIC_PH.annotv2.genotypes.vcf.gz

And I am trying to recreate vcf files with only the European samples using bcftools, but when I try

    bcftools view --samples-file 373_sampleIDs.tab GEUVADIS.chr22.PH1PH2_465.IMPFRQFILT_BIALLELIC_PH.annotv2.genotypes.vcf.gz

I get this error:

     [W::vcf_parse_format] FORMAT 'PP' is not defined in the header, assuming Type=String
     [W::vcf_parse_format] FORMAT 'BD' is not defined in the header, assuming Type=String
    Undefined tags in the header, cannot proceed in the sample subset mode.

Trying to fix it with bcftools reheader does not work:

    bcftools view -h file.vcf > header.txt; bcftools reheader -h header.txt file.vcf > fixed.vcf

I can find information on the FORMAT "PP", but not on the FORMAT "BD". 

    ##FORMAT=<ID=PP,Number=G,Type=Integer,Description="Phred-scaled Posterior Genotype Probabilities">

Would anybody be able to help?
Thanks!

the following command seems to fix the error. But I've no idea about the description of the new FORMAT. There are also some extra spaces in the INFO column...


     wget -O - "https://www.ebi.ac.uk/arrayexpress/files/E-GEUV-1/GEUVADIS.chr22.PH1PH2_465.IMPFRQFILT_BIALLELIC_PH.annotv2.genotypes.vcf.gz" |\
    gunzip -c |\
    awk '/^#CHROM/ {printf("##FORMAT=<ID=BD,Number=1,Type=String,Description=\"?\">\n##FORMAT=<ID=PP,Number=1,Type=String,Description=\"?\">\n");} {print}' |\
    sed 's/ damaging/_damaging/g'  > fixed.vcf