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Importing Variants in Alamut 1.5

Starting with version 1.5, Alamut can now import variant annotations from external sources. When variants are successfully imported they are saved as standard Alamut internal variants and can then be handled like other internal variants.

Preparing import files

In order to import variants into Alamut you have to prepare a tabular import file containing variant descriptions and annotations. Import files must follow a precise format that is most easily created using a spreadsheet application like Excel or OpenOffice Calc.

Here is an example:

The column order must be strictly observed, however only the 3 first columns are mandatory.

The header line (containing column labels) is not mandatory, but it's a good idea to keep it.

Let's review each column contents:

1. Gene — The official symbol of the gene carrying the variant.
2. Transcript — The accession number of the transcript used to describe the variant. The transcript must be known to Alamut.
3. Variant — The cDNA-level variant description, using the HGVS nomenclature. The "c." prefix is not mandatory.
4. Pathogenic — The variant classification: "no", "unknown" or "yes", if using the simple 3-classes scheme; or "CMGS/VKGL Class (1-4)", if using the CMGS/VKGL suggested classification. (If no value is supplied here, "unknown" is assumed.)
5. Patient ID — Free content field.
6. Family ID — Free content field.
7. Phenotype — Free content field.
8. Comment — Free content field.

Creating import files

When variants have been prepared in a spreadsheet application using the format described above, save the data in tab-delimited text format (e.g. in Excel: File > Save As > Save as type: Text (Tab delimited)(*.txt)).

The import process

To import variants from an import file as described above, in Alamut:

1. Open the appropriate gene and, if required, select the transcript to which variants to be imported refer.
2. Go to menu 'Mutations' > 'Import mutations...' and specify the import file you have created.

As an example, suppose you have prepared a file with gene MSH2 variants.

Before actually importing the variants, Alamut first analyzes the import file and reports valid and invalid entries as follows:

This example is somewhat contrived in order to highlight a few points:

• The first line is rejected because the transcript accession is incomplete (no version number).
• The second line is rejected firstly because it refers to gene MLH1 and not MSH2.
• The third line is rejected because the variant column is empty.
• The fourth line is rejected because the variant c.4a>G is not correct (NM_000251.1:c.4 is a G, not a A).
• The fifth line is rejected because '4 xG>A' is meaningless.
• Two lines refer to variant c.4G>C, describing two occurrences of the variant. This is correct and is the appropriate way to import occurrences.

At this step, if you click 'Import Now' the validated entries will actually get imported. A report then shows up:

Note that entries that don't add new information are marked as redundant.

2009 Interactive Biosoftware - Last modified: 5 May 2009