Playtpus and Amplicon-based panels

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Jacquelyn Reuther

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May 12, 2017, 3:57:24 PM5/12/17

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Hi,

I was testing Platypus on data generated using Illumina's TruSeq Amplicon Cancer Panel. I noticed that multiple "true positive" SNVs were not called by Platypus whereas all the indels were. I ran platypus using the filterDuplication=0 option as suggested on the wiki. Are there other options to use when analyzing amplicon-based data or was Platypus not built to handle this type of data? Thanks for your help!