svaRetro

svaRetro detects retrotransposed transcripts (RTs) from structural variant calls by identifying exon-exon junctions and insertion sites in GRanges breakend notation.

Key Features:

• RT Detection from Structural Variants: Identifies retrotransposed transcripts from structural variant calls represented in GRanges breakend notation.
• Exon-Exon Junction Analysis: Detects retrotransposed transcripts by analyzing exon-exon junctions and insertion sites.
• Event-Based Reporting: Reports candidate retrotransposed transcripts as discrete events with annotation of inserted transcript information.

Scientific Applications:

• Retrotransposed Transcript Identification: Enables detection of processed transcripts that have been retrotransposed and inserted into new genomic locations from structural variant data.
• Structural Variant Interpretation: Facilitates biological interpretation of structural variant calls by distinguishing retrotransposition events from other rearrangement types.

Methodology:

svaRetro takes structural variant calls in GRanges of breakend notation and identifies retrotransposed transcripts by exon-exon junctions and insertion sites.