snp frequency with annovar

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7.1 years ago

Stane ▴ 90

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 • 1.6k views

ADD COMMENT • link 7.1 years ago by Stane ▴ 90

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

ADD REPLY • link 7.1 years ago by DVA ▴ 630

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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 REPLY • link 7.1 years ago by Stane ▴ 90

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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 REPLY • link 7.1 years ago by Stane ▴ 90

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