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Batch Checkers

mihailefter edited this page May 23, 2019 · 1 revision

Mutalyzer Batch Checker Help

The Batch Checkers are interfaces for the different checkers that accept a large list of descriptions as input. They support submission of files containing large datasets to the Name Checker, Syntax Checker, Position Converter, and SNP Converter tools.

Batch Checker Input

The Mutalyzer Batch Checkers accept the following file formats:

  • Tab Delimited Text File
  • Microsoft Excel XML File
  • OpenOffice .odt File

The maximum file size is 10 megabytes, and the maximum length per entry (variant description) is 190 characters.

Two types of input files are accepted.

New Style

Download Example File

This file format has no header-row and no columns. Instead each row contains a single variant for the Batch check.

AB026906.1:c.274G>T

AL449423.14(CDKN2A_v002):c.5_400del

Old Mutalyzer 1 Style

Download Example File

This file format used by the Name Checker and the Syntax Checker has a header-row, which consists of three tab delimited fields. In each following row, the corresponding data is also tab delimited. The gene symbol field may be left empty, when it is not nessary to select a particular gene or transcript.

AccNo Genesymbol Mutation
AB026906.1 SDHD g.7872G>T

Users can upload files with the sequence variants to be checked. Files for the Name Checker and the Syntax Checker may contain any combination of reference sequences and sequence types for different genes. Mutalyzer's UD identifiers can also be used, but we strongly suggest updating any GenBank record following these instructions.

A message containing a link to the results will be send to the e-mail address specified, when the analysis is finished, but Mutalyzer's progress can be followed in the browser window also. Performance depends on the server load and the number of reference sequence records to be downloaded. The program will process approximately 100 variants per minute, when using a single reference sequence record.

The Batch checkers use JavaScript to update the progress report. In Internet Explorer, progress may not be reported correctly. Adding Mutalyzer to your trusted sites is one option to solve this.

Batch Checker Output Format

The output of a Mutalyzer Batch run is a CSV file, which has a header-row to clarify the results.

Note: empty lines are removed from the batch input file.

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