I've gotten back vcf files for the Michigan server. My intent was to filter the vcfs by their info value; however, it seems the vcf files don't have that specific value listed in the header:

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=2021.7.17
##contig=<ID=5>
##pipeline=michigan-imputationserver-1.5.7
##imputation=minimac4-1.0.2
##phasing=eagle-2.4
##r2Filter=0.0
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy (R-square)">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
##INFO=<ID=IMPUTED,Number=0,Type=Flag,Description="Marker was imputed but NOT genotyped">
##INFO=<ID=TYPED,Number=0,Type=Flag,Description="Marker was genotyped AND imputed">
##INFO=<ID=TYPED_ONLY,Number=0,Type=Flag,Description="Marker was genotyped but NOT imputed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##FORMAT=<ID=HDS,Number=2,Type=Float,Description="Estimated Haploid Alternate Allele Dosage">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">

Would anyone have any insights/explanation on what's going on? I'm a novice at bioinformatics so any help would be appreciated.



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