I need to mask all sites in a vcf file flagged by the 1000 Genomes Project as being unfit for population genetic analyses. The sites for all chromosomes are available at:
From above mentioned link you can get both bed files and Fasta files.
I wanted to mask all sites using VCFtools but VCFtools is not longer being updated and therefore, can't me used on the my vcf file because you can only VCFtools upto VCF file format v.2. And file format for my file is v.3. Can someone suggest another tool that I can use. Insights will be appreciated.