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 6 years ago
- A method to identify structural variation from sequencing data in target regions☆32Updated 5 years ago
- Python package and routines for merging VCF files☆29Updated 4 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Updated 3 years ago
- heuristics to merge structural variant calls in VCF format.☆38Updated 9 years ago
- ☆51Updated 6 years ago
- Simplify snpEff annotations for interesting cases☆22Updated 6 years ago
- What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.☆36Updated 2 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Updated 4 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆59Updated 8 years ago
- Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes☆31Updated 6 months ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 5 years ago
- Support Vector Structural Variation Genotyper☆58Updated 5 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 3 years ago
- Linked-Read Alignment Tool☆26Updated 6 years ago
- An awk-like VCF parser☆56Updated 2 years ago
- Pipeline for structural variant image curation and analysis.☆49Updated 4 years ago
- A collection of command line tools for working with sequencing data☆52Updated 2 weeks ago
- program for haplotype phasing from sequence reads and related tools☆25Updated 7 years ago
- Method to detect exonic CNVs in NGS Gene Targeted Panels☆16Updated 6 years ago
- Genome-wide reconstruction of complex structural variants☆39Updated 3 years ago
- Graphite - Graph-based variant adjudication☆28Updated 5 years ago
- Method for detecting STR expansions from short-read sequencing data☆63Updated 4 years ago
- BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants☆25Updated 9 years ago
- CNV detection tool for targeted NGS panel data☆16Updated 3 years ago
- A tool to benchmark mappers and different parameters within minutes☆44Updated 6 years ago
- Prioritize structural variants based on CADD scores☆29Updated 5 years ago
- Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV…☆21Updated 5 years ago
- create a gemini-compatible database from a VCF☆55Updated 5 years ago
- Structural Variant Index☆75Updated last year