I have a set of 11 vcf files derived from variant calling through snippy.
ref.vcf contains variants that I consider as background, i.e. they should all appear in the remaining vcf files.
I am interested in unique variants from sample1.vcf through sample10.vcf, in other words, report all variants not found in ref.vcf
It appears that bcftools isec tool should do that, but I am not sure how to set it up since I'm not interested in common variants but unique variants.
Would this: bcftools isec -n =11 ref.vcf.gz sample1.vcf.gz sample2.vcf.gz sample3.vcf.gz etc produce file with common varinats but also unique variants from each sample.vcf files?
Hope this is clear - thanks in advance.
Note: I have already parsed through the posts here and did not find a suitable answer for filtering unique (as opposed to common) variants.
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ThePresident
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OK - I think I might have found a reasonable solution. I can ran:
bcftools -isec -n -11 ref.vcf.gz sample1.vcf.gz sample2.vcf.gz sample3.vcf.gz etcand take a look at thesites.txtfile. I am interested in all variants that have the following signature:The "01111111111" indicates that a variant is not found in the first file but is in all the others. Not the prettiest way but gets the job done.
TP