Excluding SNPs from repetitive regions

Question

[qstefano]

Hey everyone,

I'm working with a genome with a high percentage of repetitive regions for some population genomic analyses. I want to exclude all the SNPs called in repetitive regions, do you know any software(s)? I have a VCF file containing the SNPs of the populations and the GFF.

Thanks in advance

[Pierre Lindenbaum]

if you have a BED file with those repetitive regions , use bcftools view --regions-file ^exclude.bed in.vcf.gz

[qstefano]

I don't have a BED file with repetitive regions, just the GFF.

[Pierre Lindenbaum]

I leave "converting GFF to BED with a simple awk command" to you as an exercice.