1 - 9 of 9 results

CalMaTe / Calibration Matrix T

Normalizes allele-specific copy number estimates (ASCNs) from any technology and preprocessing method, without requiring matched normal. CalMaTe is a platform-independent multi-array method that controls single nucleotide polymorphism (SNP)-specific systematic variation by modeling the crosstalk between alleles in bi-allelic SNPs. The software was applied to the TCGA-ovarian cancer dataset. An add-on to the Aroma Project framework is also included in the package.

HATS / Haplotype Amplification in Tumor Sequences

A tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next-generation sequencing tumor data. The amplified haplotype may reveal gene variants. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons in real data. We demonstrate that HATS infers the amplified alleles more accurately than does the naive approach, especially at low to intermediate coverage levels and in cases (including high coverage) possessing stromal contamination or allelic bias.


Assists users to find allele-specific copy number (ASCN) in next-generation sequencing data. FALCON uses allele-specific coverage to segment the genome. It can also detect somatic mutations that change the ASCN but not the total copy number. This method is based on a bivariate mixed Binomial process for allele-specific coverage in the two samples at heterozygous variant loci. It segments the genome into regions of homogeneous allele-specific coverage by conditioning on the matched normal sample.

FACETS / Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing

An allele-specific copy number analysis (ASCN) tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. FACETS provides a complete analysis pipeline that include BAM file post-processing steps including library size and GC-normalization, joint segmentation of total and allele-specific signals, and integer copy number calls taking into account of tumor purity, ploidy and clonal heterogeneity, all seamlessly integrated in a single workflow with comprehensive output, integrated visualization, with fast computation to facilitate large-scale application. FACETS provides a complete ASCN analysis pipeline. This is distinct from most existing methods which often require separate software packages for GC-normalization, sequencing bias adjustment and/or segmentation analysis. An integrated analysis pipeline from start to finish will provide more consistent results.

MARATHON / copy nuMber vARiAtion and Tumor pHylOgeNy

Enables copy number profiling and downstream analyses in disease genetic studies. MARATHON is a pipeline that gathers statistical software: CODEX and CODEX2 perform read depth normalization for total copy number profiling, iCNV receives read depth normalized by CODEX/CODEX2, FALCON and FALCON-X perform allele-specific copy number (ASCN) analysis and Canopy receives input from FALCON/FALCON-X to perform tumor phylogeny reconstruction. The pipeline adapts to different study designs and research goals.