platypus

platypus detects genetic variants from high-throughput sequencing data to identify SNPs, MNPs, indels, complex polymorphisms, and de novo mutations for genomic and clinical analyses.

Key Features:

• Local de novo assembly: Generates candidate variants by assembling reads locally around regions of interest, enabling detection of SNPs, MNPs, short indels, replacements, and larger deletions up to several kilobases.
• Local realignment: Performs local realignment of reads around candidate variant sites to improve the accuracy of variant calls.
• Probabilistic haplotype estimation: Estimates haplotypes probabilistically to distinguish between different genetic variations and identify complex polymorphisms and de novo mutations.
• Computational efficiency: Operates at substantially higher speed compared with tools such as SAMtools and GATK, supporting faster turnaround in clinical analyses.
• No preprocessing requirement: Generates variant calls directly from raw aligned read data without mandatory prior preprocessing steps.

Scientific Applications:

• Whole-genome and exome-capture variant discovery: Applied to whole-genome and exome-capture sequencing data for detection of SNPs, indels, and complex variants.
• Tool comparison and benchmarking: Demonstrated comparative performance against SAMtools and GATK on whole-genome and exome-capture datasets.
• De novo mutation detection in trios: Used to identify de novo variants in parent-offspring trios, including analysis of 15 trios.
• HLA genotype estimation: Capable of estimating human leukocyte antigen (HLA) genotypes directly from variant calls.

Methodology:

Performs local de novo assembly to generate candidate variants, local realignment of reads at candidate sites, and probabilistic haplotype estimation.