HemoMIPs-Automated analysis and result reporting pipeline for targeted sequencing data.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
22
01
2020
accepted:
16
05
2020
revised:
16
06
2020
pubmed:
5
6
2020
medline:
22
9
2020
entrez:
5
6
2020
Statut:
epublish
Résumé
Targeted sequencing of genomic regions is a cost- and time-efficient approach for screening patient cohorts. We present a fast and efficient workflow to analyze highly imbalanced, targeted next-generation sequencing data generated using molecular inversion probe (MIP) capture. Our Snakemake pipeline performs sample demultiplexing, overlap paired-end merging, alignment, MIP-arm trimming, variant calling, coverage analysis and report generation. Further, we support the analysis of probes specifically designed to capture certain structural variants and can assign sex using Y-chromosome-unique probes. In a user-friendly HTML report, we summarize all these results including covered, incomplete or missing regions, called variants and their predicted effects. We developed and tested our pipeline using the hemophilia A & B MIP design from the "My Life, Our Future" initiative. HemoMIPs is available as an open-source tool on GitHub at: https://github.com/kircherlab/hemoMIPs.
Identifiants
pubmed: 32497118
doi: 10.1371/journal.pcbi.1007956
pii: PCOMPBIOL-D-20-00116
pmc: PMC7297380
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1007956Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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