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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.

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Think removing everything < 0.05 from 1000g2015aug_all column of ANNOVAR annotation file helps with this

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  • $\begingroup$ It's quite rude to add and accept only your own answer after people have attempted to help you, especially when your answer is incomplete and will not help others that may have the same question. I think I will stay away from your future questions and not attempt to help you, as you seem to do this a lot (evident from your pattern on biostars, where you also ignored others' help and only accepted your own half-baked answers) $\endgroup$
    – Ram RS
    Mar 16, 2020 at 14:43
  • $\begingroup$ @RamRS you are not answering this OP's question only, but many other future users'. Keep answering, time and number of votes will point to the right answer. $\endgroup$
    – zx8754
    Mar 16, 2020 at 19:59

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