The structural variation pipeline calls structural variants in Illumina paired-end reads from whole genome mouse data relative to GRCm38 (mm10). The pipeline maps reads to the reference, and then passes mapped reads to four structural variant callers: Breakdancer, Lumpy, Delly, and Manta. Structural variant calls from the four individual callers are then merged with Survivor.

Calls are merged by type, within a +/- 1000bp buffer around each call. Merged calls provide the number of callers supporting each call.

Finally calls are annotated to include if they are within a defined exon (exons boundaries were extracted by the R package annotatr, which uses the TxDb.Mmusculus.UCSC.mm10.knownGene resource.

Annotations in that package were drawn from resources at UCSC on 2019-10-21 20:52:26 +0000 (Mon, 21 Oct 2019) and based on the mm10 genome based on the knownGene table)

Structural variant type are classed into the following types:

• INS – Insertion
• INV – Inversion
• DEL – Deletion
• DUP – Duplication
• TRA – Translocation