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Platypus specifications


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


No version available

Publication for Platypus

Platypus citations


Genomic features of renal cell carcinoma with venous tumor thrombus

Sci Rep
PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] ion as of February 2016), dbSNP (build 147), 1000 Genomes and EVS (Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA [version ESP6500SI-V2]) data. Indels were identified with Platypus callVariants (version 0.8.1, parameter settings genIndels = 1, genSNPs = 1, bufferSize = 100000 and maxReads = 10000000). All indels were annotated using Annovar (version as of November 2014) […]


Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] om NCBI GenBank no later than May 2017. For SNP finding, data were mapped using Bowtie2 v2.2.6 [] with the ‘--very-sensitive’ preset to minimise mismapped reads, and SNPs and indels were called using Platypus v0.8.1 [], setting a minimum mapping quality of 30, a minimum base quality of 20, filter duplicates to 1, and a minimum read depth to approximately 25% of the average coverage of each individ […]


EAGLE: Explicit Alternative Genome Likelihood Evaluator

BMC Med Genomics
PMCID: 5918433
PMID: 29697369
DOI: 10.1186/s12920-018-0342-1

[…] ’ [] (see Additional file  for details). We used the resulting BAM format alignment data to call variants with: GATK HaplotypeCaller (3.3.0) [, ], SAMtools mpileup (1.3) [], FreeBayes (1.0.2) [], and Platypus (0.8.1) []. Each callset was normalized using vt normalize [] and the vcfallelicprimitives module in vcflib ( to deconstruct complex variants.From the known NS12 […]


The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

Cancer Cell
PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] ese filtering steps left 988,972 SNVs and 194,250 indels. We further genotyped these across our panel of 30 low-coverage normal devil genomes and 12 previously published normal devil genomes () using Platypus with settings --minPosterior=0 and --minReads=0. […]


Insights into Platypus Population Structure and History from Whole Genome Sequencing

Mol Biol Evol
PMCID: 5913675
PMID: 29688544
DOI: 10.1093/molbev/msy041

[…] Stampy () without BWA premapping. Duplicates were removed using Picard MarkDuplicates tool ( Variant calling was performed jointly on the 58 samples using the PLATYPUS variant caller (Rimmer et al. 2014), and we obtained a total of 14,127,611 biallelic SNPs with the “PASS” filter. We removed indel calls, monomorphic positions, and 2042 positions where the r […]


The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome

Sci Rep
PMCID: 5807544
PMID: 29426844
DOI: 10.1038/s41598-018-20783-6

[…] gainst the Populus trichocarpa reference genome v.3.0 using BWA v0.7.13, together with Samtools v0.1.19 to produce an alignment file for each individual tree. Haplotype variants were then called with Platypus v0.8.1 and filtered using the R package stackr v0.5.3. Eleven more individuals that yielded doubtful results were removed from the data set, leaving 309 individuals for genetic data analyses. […]


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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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