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SNP and INDEL VariantFiltration Parameters

teodora_aleksicteodora_aleksic SerbiaMember
edited April 2017 in Ask the GATK team

Hi,

I've been looking for recommended filter expressions for SNP and INDEL variant filtration. I found these articles on the topic: one and two. I noticed that in the second article the SOR annotation is recommended for both SNP and INDEL filtration, while in the first article it is not. I would like to know which of these filter expressions would be considered Best Practice for variant filtration.

Thanks,
Teodora

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