melbournebioinformatics / variant_calling_pipelineLinks
A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framework in Python.
☆34Updated 11 years ago
Alternatives and similar repositories for variant_calling_pipeline
Users that are interested in variant_calling_pipeline are comparing it to the libraries listed below
Sorting:
- Method for detecting STR expansions from short-read sequencing data☆63Updated 3 years ago
- Tools for next-generation sequencing analysis☆89Updated 6 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated 2 years ago
- Simplify snpEff annotations for interesting cases☆22Updated 6 years ago
- smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…☆20Updated 6 years ago
- Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing☆41Updated 6 years ago
- Multi-sample somatic variant caller☆52Updated 3 years ago
- ☆51Updated 6 years ago
- Mapped QC analysis program☆44Updated 7 years ago
- Maximum likelihood demultiplexing☆47Updated 7 months ago
- Remove primer sequence from BAM alignments by soft-clipping☆31Updated 5 years ago
- ☆78Updated 11 years ago
- A Framework to call Structural Variants from NGS based datasets☆22Updated 7 years ago
- Splice junction analysis and filtering from BAM files☆42Updated 3 years ago
- (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER☆31Updated 6 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
- Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at rea…☆26Updated 5 years ago
- A snakemake pipeline for SV analysis from nanopore genome sequencing☆51Updated 5 years ago
- De novo transcriptome assembler for short reads☆63Updated 7 years ago
- A software for calculating telomere length☆71Updated 6 years ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 3 years ago
- Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.☆24Updated 11 years ago
- A method to identify structural variation from sequencing data in target regions☆32Updated 4 years ago
- Tools for analyzing 10X Genomics data☆42Updated 6 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆21Updated 5 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 9 years ago
- Miscellaneous Bioinformatics scripts etc mostly in Python☆45Updated 2 weeks ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Updated 4 years ago
- full taxonomer cython repository☆22Updated 5 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 8 years ago