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Old 01-12-2015, 11:50 PM   #1
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Location: Montpellier

Join Date: Jan 2015
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Default varFilter -D option setting


Could somebody give me advices about the good practices to set the option "-D" of the varFilter script (from samtools/bcftools)? I have read that the option is useful to remove false positive SNPs due tu alignement artifacts, and that it must be set in function of the coverage you have in your data. If I have a mean coverage of 40X, how should I preferably set -D? -D80, -D120, ...?

Thank you for your help !

Cahuette is offline   Reply With Quote

parameter tuning, samtools, variant filtering

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