cancerit / CaVEMan
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
☆61Updated last week
Alternatives and similar repositories for CaVEMan:
Users that are interested in CaVEMan are comparing it to the libraries listed below
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Updated 9 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Updated 4 years ago
- SV clustering☆28Updated 3 years ago
- ☆78Updated 11 years ago
- Run Picard on BAM files and collate 90 metrics into one file.☆41Updated 7 years ago
- Battenberg algorithm and associated implementation script☆52Updated 4 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…☆66Updated 2 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Fast fusion detection using kallisto☆80Updated 6 months ago
- Mapped QC analysis program☆44Updated 6 years ago
- Method for detecting STR expansions from short-read sequencing data☆62Updated 3 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆55Updated 7 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆50Updated 2 years ago
- An awk-like VCF parser☆56Updated last year
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 7 years ago
- ☆35Updated 4 years ago
- ☆46Updated 5 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- small RNA analysis from NGS data☆37Updated 8 months ago
- Version II of Mandalorion☆32Updated 6 years ago
- Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel☆28Updated 7 months ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- Quality of RNA-Seq Toolset☆53Updated 6 years ago
- BigWig and BAM utilities☆96Updated 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…☆44Updated 2 years ago
- a wee tool for random access into BGZF files.☆84Updated 6 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 8 years ago