uci-cbcl / PyLOH
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
☆39Updated 7 years ago
Alternatives and similar repositories for PyLOH:
Users that are interested in PyLOH are comparing it to the libraries listed below
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆50Updated 2 years ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆53Updated 7 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 8 years ago
- ☆46Updated 5 years ago
- for detecting internal tandem duplication from genome sequence data.☆11Updated 5 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- Microsatellite instability (MSI) detection for cfDNA samples.☆19Updated 4 years ago
- Concordance and contamination estimator for tumor–normal pairs☆58Updated 6 months ago
- heuristics to merge structural variant calls in VCF format.☆36Updated 8 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆21Updated 4 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- CN-Learn☆29Updated 5 years ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆25Updated 8 years ago
- ☆41Updated last year
- Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.☆27Updated 3 years ago
- ☆68Updated 2 years ago
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 6 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- for visual evaluation of read support for structural variation☆52Updated 11 months ago
- an empirical Bayesian framework for mutation detection from cancer genome sequencing data☆31Updated 9 years ago
- SMN1 copy-number and sequence variant analysis from next generation sequencing data☆22Updated last year
- FLT3 ITD detection (ITDseek) and simulation (ITDsim)☆14Updated 6 years ago
- ☆51Updated 5 years ago
- Assembly Based ReAligner☆73Updated 6 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- A tool for simulating CNVs for WES data. It simulates rearranged genome(s), short reads (fastq) and BAM file(s) automatically in one sing…☆17Updated 5 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago