filtering repetitive regions with low quality/no snps in a vcf file

Question

[peter]

I have a vcf file and I want to filter for repetitive regions with low quality or no SNPs in my vcf file. I have a repeat masker bed file for repeats but I don't know how to use that for repetitive regions. How can I eliminate sites masked by RepeatMasker? Insights will be appreciated.

[timothy.delory]

Hi Peter,

Did you ever end up working this one out? I am trying to make a .bed file with the location of all repetitive regions of contig, so that I can mask these repeat regions for another analysis.

Cheers,

Tim

[peter]

Hi. I ended up using bedops for example:

$ bedops --chrom chr14 -n 1 <(vcf2bed < variants.vcf) <(sort-bed repeats.bed) > answer.bed
$ bedops --chrom chr14 -n 1 <(vcf2bed < variants.vcf) <(rmsk2bed < repeats.rmsk) > answer.bed

Let me know if this helps or if you came across a better solution.