friend1ws / EBCall
an empirical Bayesian framework for mutation detection from cancer genome sequencing data
☆31Updated 8 years ago
Related projects ⓘ
Alternatives and complementary repositories for EBCall
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- An awk-like VCF parser☆54Updated 10 months ago
- Python package and routines for merging VCF files☆29Updated 3 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 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
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated this week
- Pipeline for structural variation detection in cohorts☆48Updated 3 years ago
- For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…☆33Updated last year
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆77Updated 9 months ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆54Updated 7 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
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- R package for inferring copy number from read depth☆31Updated 2 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 2 years ago
- Concordance and contamination estimator for tumor–normal pairs☆56Updated 3 weeks ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- heuristics to merge structural variant calls in VCF format.☆35Updated 8 years ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Detection of Circular RNA and Fusions from RNA-Seq☆32Updated 6 years ago
- ☆51Updated 5 years ago
- ☆45Updated 5 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 4 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆41Updated 2 years ago
- ☆78Updated 10 years ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆74Updated last year
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆43Updated 2 years ago
- for visual evaluation of read support for structural variation☆50Updated 5 months ago
- Burden testing against public controls☆50Updated 8 months ago
- Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.☆27Updated 3 years ago