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Main Settings Presets

This section describes the main settings presets that are used for analysis. Some of them may have been added to your profile by an administrator when registering in the system. If you need other preset described here for analysis, you can contact your administrator or create it yourself, as described below.

1. Somatic and germline variant analysis {#somаtic-and-germline-variant-analysis}#

  • allows somatic and germline mutations (SNVs/indels), structural variations and copy number variations discovery;
  • completely identical to the preset that is created by default (before any changes are made to it);
  • suitable for the analysis of any samples in any file format.

If you want to create such a preset yourself, do the following:

  1. On the "Settings presets" page, click on to open the form for a preset adding.

  2. In the opened form, enter settings preset name ("Somatic and germline variant analysis") in the "Name" field.

  3. Click on . Because this preset is the same as the default preset, no further changes need to be made and you can leave the page.

2. Germline variant analysis#

  • allows germline mutations (SNVs/indels), structural variations and copy number variations discovery;
  • differs from the preset that is created by default by the analysis mode - Germline variant analysis, which does not provide for somatic mutations and variations discovery in samples;
  • suitable for the analysis of normal (non-tumor) samples in any file format.

If you want to create such a preset yourself, do the following:

  1. On the "Settings presets" page, click on to open the form for a preset adding.

  2. In the opened form, enter settings preset name ("Somatic and germline variant analysis") in the "Name" field.

  3. Click on .

  4. On the opened preset page, change analysis mode to "Germline variant analysis":

3. Prenatal analysis#

  • allows germline aneuploidies (variations in the number of copies of chromosomes) discovery;
  • differs from the preset that is created by default by the analysis mode - Germline variant analysis, which does not provide for somatic mutations and variations discovery in samples, and by disabled germline SNVs/indels and structural variations discovery;
  • suitable for the analysis of normal (non-tumor) samples in FASTQ or BAM files.

If you want to create such a preset yourself, do the following:

  1. On the "Settings presets" page, click on to open the form for a preset adding.

  2. In the opened form, enter settings preset name ("Somatic and germline variant analysis") in the "Name" field.

  3. Click on .

  4. On the opened preset page, change analysis mode to "Germline variant analysis":

  1. Disable germline SNVs/indels discovery by turning off the corresponding toggle:

  1. Disable structural variations discovery by turning off the corresponding toggle:

  1. Limit the copy number variations discovery to the discovery of only germline aneuploidies by turning on the corresponding toggle: