I have a set of vcf files that were filtered using GATK hard filtering. I filtered the snps and then the indels seperately and then merged the two and got a vcf with a list of polymorphisms in which the polymorphisms that had failed the filters weere marked as such (of course)  Now I would like to make a vcf that lacks the snps and Indels that failed the filtering. What command should I run. 
If you're referring to the `PASS` flag, you can use anything from `vcftools` to plain `awk` to plainer `grep`. If there's more to the PASS criteria than just the flag, you're going to need to elaborate on that.

Also, do you mean `variants` when you say `polymorphisms`? I know people may use the terms interchangeably, but they do not mean the same thing. `Variants` are the most generic descriptor; they refer to all loci where multiple alleles are found, whereas `polymorphisms` assume the functional impact of the variant to result in a polymorphic phenotype that is not usually pathogenic.