statgen / gotcloud
Genomes on the Cloud, Mapping & Variant Calling Pipelines
☆32Updated 7 years ago
Related projects: ⓘ
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- An awk-like VCF parser☆54Updated 8 months ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆47Updated 5 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆28Updated 3 years ago
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 5 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆31Updated 8 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 3 years ago
- ☆22Updated last month
- Pipeline for structural variation detection in cohorts☆45Updated 3 years ago
- A method to identify structural variation from sequencing data in target regions☆31Updated 3 years ago
- gnomAD browser pre-ASHG 2018☆33Updated 3 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated last year
- Burden testing against public controls☆49Updated 6 months ago
- heuristics to merge structural variant calls in VCF format.☆35Updated 7 years ago
- an empirical Bayesian framework for mutation detection from cancer genome sequencing data☆31Updated 8 years ago
- ☆44Updated 4 years ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆51Updated 7 years ago
- Python package and routines for merging VCF files☆29Updated 3 years ago
- R package for inferring copy number from read depth☆30Updated last year
- SMN1 copy-number and sequence variant analysis from next generation sequencing data☆21Updated last year
- QDNAseq package for Bioconductor☆45Updated last month
- Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets☆37Updated 4 years ago
- ☆24Updated 3 months ago
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆24Updated 8 months ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 7 years ago
- CAVA (Clinical Annotation of VAriants)☆14Updated 5 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 4 years ago
- ☆22Updated this week
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago