HTS Bioinf - ELLA INS module
Scope
This document describes the insertion (INS) variants that are displayed in ELLA for EKG users.
Summary of INS variant processing
This pipeline displays INS variants in a table in the ELLA INFO page. Only variants in BRCA1 or MSH2 are shown for the EKG genepanels that include these genes.
Processing steps
INS variant calling
The INS variants are called by the SV caller of the Dragen pipeline stage of basepipe.
Quality control
No quality control (QC) has been performed, and the user has to inspect the site of the INS variant in the BAM file track of the ELLA CNV module visual.
Final output and reporting
The INS variants are displayed in the ELLA INFO page in a table format. The table contains the following columns:
| Field | Description |
|---|---|
| chrom | Chromosome of the variant |
| pos | Position of the variant |
| id | ID of the variant, starting with "INS" or "BND" |
| qual | Quality score of the variant |
| filter | Filter status of the variant |
Notes
- Whenever an analysis is not automatically finalized, there could potentially be a variant in this table.
- In order to verify the variant, the user can inspect the BAM file track of the ELLA CNV module visual. There are no visual tracks for the INS variants.
- In addition to the INS variants, for the MSH2 gene, there might also be BND variants. These variants are recognied by the presence of a "BND" in the ID column. The reason that these variants are shown is that the INS variant in the MSH2 gene is 39kb, which means that it will not be called directly, but has to be inferred by combining information found in the MSH2 gene with the presence of a 39kb DUP between MSH2 and MSH6. In addition, the region between the INS and the DUP could be inverted. This inversion is called by an assebly of 4 BND variants. The variant can also be falsely called as a 250kb DEL that approximately spans the region between the INS and the DUP. The DUP itself is not available in ELLA because it falls between gene panels. In other words, the presence of any INS or BND in the MSH2 only indicates the presence of the expected 39kb INS.