Remove repetitive region vcf file using repeatmasker bed file
A couple fast alternatives:
$ bedops --chrom chr14 -n 1 &lt;(vcf2bed &lt; variants.vcf) &lt;(sort-bed repeats.bed) &gt; answer.bed
$ bedops --chrom chr14 -n 1 &lt;(vcf2bed &lt; variants.vcf) &lt;(rmsk2bed &lt; repeats.rmsk) &gt; answer.bed

Using --chrom chr14 focuses set operations on that chromosome.