An integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing

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Parameters selection:

De novo SNV

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• For the de novo SNV identification of VCF file, there are several parameters that users can set for calling, such as quality, depth, QD, MQ0, PL, Hrun, which are detailedly described in here. While the parameter of "Flank" used for filtering SNV around the INDEL. "PRT" and "PART" used for genotype control.

De novo INDEL

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• The parameters are similar as "De novo SNV".

Rare inherited calling

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• The parameters of "quality" and "depth" are the same as above. While the "Database" is used for alternative allele frequency filtering.

Risk gene prediction

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• mirTrios selects 12 kinds of software for variants damage predicting automatically. The mutation will be defined as damaging once 8 or more softwares render as such. Only predicted damaging missenses and loss of function variants are used for risk gene prediction by TADA.

Non-coding region analysis

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• The parameters for non-coding region analysis.

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