Ngs ExtractGenotypeFromVcfData.pdf

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Extract Genotypes From VCF Data

Overview

Extract Genotype From VCF Data allows the user to extract SNP data from VCF Data objects. The SNP results can be used to do genotyping analysis.

To access this module, please go to Analysis | NGS | Variation | Extract Genotypes From VCF Data

ExtractGenotype Menu.png

Input Data Requirements

Thie module requires a VCF Data object. VCF data objects can be added using Add VCF Data module.

General Options

ExtractGenotype.png

Input/Output

  • Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
  • References:Selections can be made on which references, such as chromosomes, should be included in the filtering (options include All references, Selected references, Visible references, and Customized references (select any pre-generated Lists))
  • Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pre-generated Lists).
  • Output name: The user can choose to name the output data object.


Options

  • Quality Cutoff: cutoff for QUAL, the phred-scaled quality score for the assertion made in ALT.
  • Filter Cutoff: Select VCF entries based on the FILTER column. Leave it empty to select all mutations in the VCF file.
  • Coverage Cutoff: Select VCF entries based on the DP values.
  • Frequency Cutoff: Select VCF entries based on the AF values.
  • Call No-genotype as reference homogenous: if checked the sample will be treated as wild type if the mutation is not present in its VCF file but shown in other samples' VCF files.

SNP calls will be missing, using ".", if sample does not pass any of above filters.

Output Results

The SNP results will be an -Omic data object that can be used to do genotyping analysis.

20131015 ExtractSNPFromVCF Result.png

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