Remove repetitive region vcf file using repeatmasker bed file I have a 1000 genomes vcf file for chromosome 14. And I want to remove variants in repetitive regions flagged by repeatMasker. I have a bed file for those repeats. I downloaded that file from UCSC. How can I eliminate/remove those sites in vcf file using repeat masker's bed file? Insights will be appreciated.
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.