LoLoPicker specifications

Information


Unique identifier OMICS_11396
Name LoLoPicker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
PySam, PySamstats
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jian Carrot-Zhang

Publication for LoLoPicker

LoLoPicker citation

library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] the probability of observing more non-reference reads than nT. Because somatic variants are known to be enriched in certain hot-spots, sequence contexts, and non-coding regions, EBCall, deepSNV, and LoLoPicker estimate site-specific error rates and therefore allow distinct and more accurate detection limit at each site. In particular, deepSNV and LoLoPicker are designed to call low-frequency vari […]

LoLoPicker institution(s)
Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Human Genetics, McGill University, Montreal, QC, Canada; Genome Quebec Innovation Centre, Montreal, QC, Canada
LoLoPicker funding source(s)
Supported by the Canadian Institutes of Health Research [grant number 77764]; by the CIHR postdoctoral fellowship; and by a Canada Research Chair in Genomics.

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