Closed
Description
I have a VCF that includes a String FORMAT tag like this:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=VF,Number=A,Type=Float,Description="Variant Frequency">
##FORMAT=<ID=STR,Number=A,Type=String,Description="String that goes missing">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
chr1 150 . TAT CCC 100 PASS AC=1;AN=2;TYPE=MNP GT:VF:STR 0/1:0.1:DATA
When I do bcftools norm -a in.vcf, it removes the STR tag. Is this intended behavior, and am I being cavalier with the FORMAT field? TMI: The reason I'm not using INFO/STR is because this feeds into Illumina's hap.py engine, which adds INFO/TRUTH_FMT and INFO/QUERY_FMT for each variant to the output VCF.
Thanks!