Platypus protocols

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Platypus computational protocol

Platypus specifications

Information


Unique identifier OMICS_00068
Name Platypus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Cython, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Platypus

Platypus IN pipelines

 (12)
2018
PMCID: 5761188
PMID: 29316957
DOI: 10.1186/s13058-017-0929-z

[…] recalibration and indel realignment performed using the genome analysis toolkit (gatk v3.2.2) [21]. gatk unifiedgenotyper v2.4 (broad institute, cambridge, ma, usa) [22], haplotypecaller [23] and platypus [24] were used for variant calling. annotation of variants was performed using a local copy of the ensembl [25] version r73 database and a customised version of ensembl variant effect […]

2017
PMCID: 5617183
PMID: 28953922
DOI: 10.1371/journal.pone.0185103

[…] and converted to bam with piccard and the alignment was recalibrated following the broad institute recommended best practices [10, 11]variants were called using haplotype caller (gatk) [12] and platypus[13]. structural variants (big deletion or insertions among the amplified fragments) were called with delly2[14]. the resulting vcf files were annotated with structural information […]

2017
PMCID: 5736667
PMID: 29259247
DOI: 10.1038/s41467-017-02177-w

[…] tag in dbsnp or > 1% frequency in exac 0.3.1) were filtered out and only high-confidence mutations in the coding regions were kept. calling of small insertions/deletions (indel) was performed by platypus 0.8.1 using the same filtering process as with the snv calling65. both snv and indel calling were performed without using paired germline control samples. the data were plotted […]

2016
PMCID: 4906373
PMID: 27239039
DOI: 10.1016/j.celrep.2016.04.090

[…] paired-end reads were mapped using stampy (lunter and goodson, 2011), and duplicate pcr reads were removed using picard (http://picard.sourceforge.net/). single-nucleotide variants were called using platypus (rimmer et al., 2014)., c57bl/6j wild-type mice were bred, housed, and time mated according to standard operating procedures approved by the animal ethics committee at monash university […]

2016
PMCID: 4915495
PMID: 26818911
DOI: 10.1002/jbmr.2797

[…] to the human sequence version 37d5 (hs37d5) reference genome using stampy17 and variant calling of single nucleotide variants (snvs) and short insertions and deletions (indels) was undertaken using platypus (v0.5.1).18 analysis of coding variants was undertaken using ingenuity variant analysis. to search for variants causing hypocalcemia and keratoconus under autosomal dominant inheritance […]

Platypus institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK

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