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3.12 Import Scripts

Three import scripts are provided by default in SVS. Additional import scripts may be available for specific data import situations. See Download Menu for more information on obtaining scripts.

HapMap

This script imports user-specified text files with extensions .txt or .csv from the HapMap project. Multiple HapMap files cannot be merged together with this script.

Illumina Final Report by SNP

This script imports a user-specified file in one of the many Illumina text formats, which can be exported using the Final Report wizard in Illumina’s BeadStudio or GenomeStudio Software.

For this script to work properly, data needs to be exported in the following order: SNPID, PatientID, Call1, Call2, Confidence. The data has to be grouped by SNP, but the file can be comma or tab delimited. Genotype calls can be in a number of formats including: Allele - Top, Allele - Forward, Allele - Design, Allele - AB. Missing values are represented as a dash -.

The exported file will contain file information, a header line and then the genotype data.

When you run this script, you will be prompted to choose a file to import. Once chosen you will be asked to specify whether your file is tab or comma delimited, if you want to use a GC Score (Gene Calling Score) threshold to drop SNPs. If you choose to use a GC Score threshold, a second dialog box will appear asking you to to input your threshold value (range: 0 - 1). SNPs with a GC Score below this threshold will be imported as missing values (?_?).

The SNPs will be saved in the spreadsheet in the order they appear. You will still want to import a marker map and apply it to get a reordered spreadsheet.

Parallele Long File

This script imports a user-specified text file (either CSV or TXT) generated from Parallele.

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