I'm trying to write some vcf parsing code using allel. My problem at the moment is that if the VCF has a '.' instead of a 'PASS', it gets translated into FALSE. Is there a way to see the real column data? Not every VCF will have had filters applied to it, but the current functionality doesn't allow me to check if it was a true fail or just empty.
I'm trying to write some vcf parsing code using allel. My problem at the moment is that if the VCF has a '.' instead of a 'PASS', it gets translated into FALSE. Is there a way to see the real column data? Not every VCF will have had filters applied to it, but the current functionality doesn't allow me to check if it was a true fail or just empty.