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Old 04-27-2015, 02:38 AM   #1
polgimenez
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Location: Barcelona

Join Date: May 2012
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Default Annovar and variants with a MAF = 1 in fileterd file

Hi,

I'm a new user of annovar.
When I filter with 1000 genomes database using the following command:
perl annotate_variation.pl -filter -dbtype 1000g2014oct_eur -buildver hg19 my.vcf humandb/ -maf 0.01.
In the filteted file I have the variants with a MAF lower than 0.01, but also the variants with a MAF equal to 1.
Why the variants with a MAF of 1 appear here (in filtered file).
For me it not make sense because I' m looking for ômutationsö. Perhaps the answer is obvious but I don't see it.


PD: I have searched previous post about annovar and I haven't found the answer, perhaps I have missed some of them.
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