xuchang116 / smCounterLinks
smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3425-4
☆20Updated 6 years ago
Alternatives and similar repositories for smCounter
Users that are interested in smCounter are comparing it to the libraries listed below
Sorting:
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years 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.☆36Updated 8 years ago
- Simplify snpEff annotations for interesting cases☆22Updated 6 years ago
- create a gemini-compatible database from a VCF☆56Updated 4 years ago
- A method to identify structural variation from sequencing data in target regions☆32Updated 4 years ago
- Python package and routines for merging VCF files☆29Updated 4 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated 2 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Updated 3 years ago
- Thousand Variant Callers Project Repository☆73Updated 5 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Updated 4 years ago
- What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.☆33Updated 2 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆58Updated 8 years ago
- program for haplotype phasing from sequence reads and related tools☆25Updated 6 years ago
- CAVA (Clinical Annotation of VAriants)☆14Updated 6 years ago
- Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes☆31Updated last month
- ☆29Updated 4 years ago
- BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants☆25Updated 9 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 3 years ago
- Automated human exome/genome variants detection from FASTQ files☆22Updated 3 years ago
- RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…☆67Updated 2 years ago
- Tools for analyzing 10X Genomics data☆42Updated 6 years ago
- An awk-like VCF parser☆56Updated last year
- A tool to benchmark mappers and different parameters within minutes☆44Updated 6 years ago
- for visual evaluation of read support for structural variation☆54Updated last year
- filtering trio-based genetic variants in VCFs for clinical review☆21Updated 5 years ago
- ☆51Updated 6 years ago
- Mapped QC analysis program☆44Updated 7 years ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Updated last year
- Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets☆37Updated 5 years ago