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Trfermikit: a tool to discover VNTR-associated deletions.

ABSTRACT:

Summary

We present trfermikit, a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. In such regions, it achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta and complements it by recovering a significant number of deletions that Manta missed. trfermikit is based upon the fermikit pipeline, which performs read assembly, maps the assembly to the reference genome and calls variants from the alignment.

Availability and implementation

https://github.com/petermchale/trfermikit.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: McHale P

PROVIDER: S-EPMC8826174 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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trfermikit: a tool to discover VNTR-associated deletions.

McHale Peter P Quinlan Aaron R AR

Bioinformatics (Oxford, England) 20220201 5

<h4>Summary</h4>We present trfermikit, a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. In such regions, it achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta and complements it by recovering a significant number of deletions that Manta missed. trfermikit is based upon the fermikit pipeline, which performs read assembly, maps th ...[more]

PMID: 34864893

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