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Old 09-02-2016, 12:58 AM   #1
tristan dubos
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Location: France

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Post Annovar variant filtering

He guys,
I m using convert2annovar.pl to convert vcf to avinput , and in this output i have only 14 variants against more then 1000 variants in the input.
Do you know witch filters apply convert2annovar.pl to reduce the number of variant ?

Best regards

Tristan
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Old 09-02-2016, 03:31 AM   #2
vivek_
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I don't think there is a filter involved in the conversion, anyways you should get a .log file that tells you all that annovar did on the dataset.
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Old 09-02-2016, 03:47 AM   #3
tristan dubos
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Thank you for the answer. There is not log file during the conversion (with default mode) i think the log file is create during the annotate_variation.pl
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