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ANNOVAR annotation
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Unique SNP sharing between populations
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did you add "-allsample" argument to your command?
nop as I didn't want x separate output files. I did run convert2annovar.pl with the -withfreq option but the result is not very good, there is even no column name
The frequency computed in convert2annovar.pl are somehow correct, it divide the snp appearance on the population by 2 times the total number individual which makes sense as 2 alleles per individual, but now my problem is that denominator to be 2 times pop minus the missing call for this snp