ding-lab / BreakPointSurveyor
A comprehensive pipeline to analyze and visualize structural variants
☆20Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for BreakPointSurveyor
- Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA☆25Updated 5 months ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆56Updated 2 years ago
- Prioritize structural variants based on CADD scores☆28Updated 4 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 6 years ago
- VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…☆22Updated 4 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Updated 10 months ago
- Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes☆27Updated 4 months ago
- Structural variant VCF annotation, duplicate removal and comparison☆27Updated 2 months ago
- Python package and routines for merging VCF files☆29Updated 3 years ago
- Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV…☆20Updated 4 years ago
- Pipeline for structural variant image curation and analysis.☆48Updated 2 years ago
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Updated 3 months ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 2 years ago
- Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation☆22Updated 5 years ago
- FermiKit small variant calls for public SGDP samples☆17Updated 8 years ago
- Exploration of controlled loss of quality values for compressing CRAM files☆34Updated last year
- Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.☆24Updated 10 years ago
- Structural Variation breakpoint discovery via adaptive learning☆15Updated last year
- heuristics to merge structural variant calls in VCF format.☆35Updated 8 years ago
- Structural Variant Prediction Viewer☆31Updated 7 years ago
- SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.☆16Updated 6 years ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 4 years ago
- ☆21Updated 3 months ago
- v2.x of the microassembly based somatic variant caller☆14Updated 2 months ago
- picking up low allelic-fraction, somatic variants from tumor samples☆14Updated 6 years ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆17Updated 4 years ago
- A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)☆13Updated 6 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer☆21Updated 3 years ago
- Wrapper for RTG's vcfeval; DEPRECATED!☆21Updated 8 years ago