BasePlayer pipeline

BasePlayer specifications

Information


Unique identifier OMICS_17485
Name BasePlayer
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Affero General Public License version 3
Computer skills Basic
Stability Stable
Source code URL https://codeload.github.com/rkataine/BasePlayer/zip/master
Maintained Yes

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Publication for BasePlayer

BasePlayer IN pipelines

 (2)
2017
PMCID: 5397753
PMID: 28427458
DOI: 10.1186/s40246-017-0102-x

[…] short-indel variants were then called using gatk haplotypecaller., the snv and indel variants in the exome sequencing data were analyzed with an in-house developed analysis and visualization tool (baseplayer, katainen et al., manuscript in preparation). a minimum coverage of four reads and the mutated allele present in at least 20% of the reads was required to call a variant. the variants […]

2017
PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] as grch37 coordinates 22:29065455–29066124. to examine whether the novel candidate insertions were detected by wgs or not, we performed a thorough visual inspection of the paired-end read data using baseplayer32., in order to compare ldi-pcr nanopore sequencing results to wgs data we performed local assembly of the wgs data. we selected those chimeric reads and discordant read pairs that aligned […]

BasePlayer institution(s)
Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Finland; Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland; Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Finland
BasePlayer funding source(s)
This work was supported by grants from the Biomedicum Helsinki Foundation; Cancer Society of Finland; Emil Aaltonen Foundation; the Sigrid Juselius Foundation; Academy of Finland (Finnish Center of Excellence Program 2012–2017) [250345]; the European Research Council (ERC) [268648]; a European Union Framework Programme 7 Collaborative Project (SYSCOL) [258236]; the Nordic Information for Action eScience Center (NIASC); and a Nordic Center of Excellence financed by NordForsk [62721].

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