report_generation.md

Report generation

In order to configure a report, report meta data (called report configuration) for individual variants can be set. This report configuration is used to generate reports and variant sheets.

Configuring report variants

The report configuration of a sample can be opened by:

• double-clicking the header field of a variant or
• though the context menu of the variant line (or the header field)

The report configuration contains information about the variant type:

• diagnostic variant
• candidate variant
• incidental finding

Additionally, this information is stored:

• if the variant is causal for the phenotype
• inheritance information (inheritance mode, de-novo, ...)
• reason why the variant is not shown in the report (artefact, ...)
• comments of the first/second person that analyzes the sample

Persistent storage of report configurations

The report configuration of a sample is automatically stored in the NGSD whenever it is modified. It is loaded automatically loaded the next time the sample is opened.

Attention: Do not work on the report configuration of the same sample from two or more instances of GSvar. This can lead to data loss!!

Manual curation of variants

In the report configuration you can manually changes some aspects of the variants.

This is usually necessary for example in these cases:

• a complex small variant are split into several variants during variant normalization.
• a large CNV is split into several CNVs because it contains regions that are copy-number polymorphic.
• the genotype of a small variant, a CNVs or a SVs is not correctly detected.

Generally, if a single variant is split into several variants, exclude all but one of the fragments from the report using other reason and document that the variant belongs to a splot variant in the comments.

Manual curation of small variants

For small variants the following properties can be changed:

• the variant itself (the coordinates have to be near the original variant though)
• the genotype

This is the respective part of the report configuration dialog:

The button on the right is used to import a variant in several formats (GSvar, VCF, HGVS.c).

Manual curation of CNVs

For copy-number variants the following properties can be changed:

• the start position
• the end position
• the copy-number
• the HGVS type
• the HGVS suffix (after type)

This is the respective part of the report configuration dialog:

Manual curation of SVs

For structural variants the following properties can be changed:

• the start position
• the end position
• the genotype
• the start position of the second breakpoint (BND only)
• the end position of the second breakpoint (BND only)
• the HGVS type
• the HGVS suffix (after type)

This is the respective part of the report configuration dialog:

Generating a report or evaluation sheet

Through the report menu, a report for the sample can be generated:

Additionally, a evaluation sheet can be stored as documentation of the variant analysis of the sample. It opens a dialog which has to be filled with details of the analysis and creates a HTML document which contains all variant that have a report configuration including comments.