I have 15 .vcf files. I need to remove `common variants in the 1000 genomes database' appearing in at least 0.5% of the population
Do you know from where I may start?
Thank you so much
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Use VEP, ANNOVAR or snpEff to annotate your VCF file (I'd recommend combining your VCFs into a single file if they're single sample VCFs or are all comprised of samples from the same experiment/cohort). You can annotate the VCF file with 1000g (among a ton of other annotation sources). Once done, you can use
bcftools view to subset the VCF as required.
Or, you can subset the standalone 1000g VCF and pick regions with your frequency threshold, then you can use that regions file to subset your VCF file(s).
Remember to left-align and normalize (and split multi-allelic records in) your VCF files so all comparisons can be done accounting for chr, pos, ref and alt fields.