Question: snp frequency with annovar
0
gravatar for Stane
2.2 years ago by
Stane70
Europe
Stane70 wrote:

Is it possible to get the snp frequency from a vcf population file ? I have been trying to add -withfreq to the table_annovar.pl command but it is not working

snp • 660 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Stane70

did you add "-allsample" argument to your command?

ADD REPLYlink written 2.2 years ago by DVA510

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Stane70

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Stane70
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