PACT: a pipeline for analysis of circulating tumor DNA.
Bioinformatics
; 39(8)2023 08 01.
Article
in En
| MEDLINE
| ID: mdl-37549060
ABSTRACT
MOTIVATION Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants. RESULTS:
We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments. AVAILABILITY AND IMPLEMENTATION PACT is freely available at https//github.com/ChrisMaherLab/PACT.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Circulating Tumor DNA
/
Neoplasms
Limits:
Humans
Language:
En
Journal:
Bioinformatics
Year:
2023
Document type:
Article