Meerkat

Overview

Meerkat is a computational tool for detecting somatic structural rearrangements (translocations, inversions, deletions, duplications) from paired-end whole-genome sequencing data using split-read and discordant read-pair signals.

Used by

• Used in the TCGA ChRCC project to detect structural rearrangements from 50 WGS tumor/normal pairs (mean 16 rearrangements per case, range 0–207); identified recurrent genomic rearrangement breakpoints within ~10 kb upstream of the TERT transcription start site in 6/50 cases, a novel TERT-upregulation mechanism. PMID:25155756
• Meerkat used alongside BreakDancer for structural-variant detection in the TCGA esophageal/stomach study of 164 oesophageal carcinomas PMID:28052061.

Notes

• Detects genome rearrangements from short-read WGS; outputs breakpoint positions and rearrangement classes.
• Used alongside kataegis identification in ChRCC; rearrangement breakpoints co-localized with APOBEC-pattern mutation clusters in a subset of cases.

Sources

This page was processed by entity-page-writer on 2026-05-11. - PMID:28052061

This page was processed by wiki-cli on 2026-05-14.