dkoboldt / varscan
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
☆156Updated last year
Alternatives and similar repositories for varscan:
Users that are interested in varscan are comparing it to the libraries listed below
- VarDict☆194Updated last year
- Script to automatically create and run IGV snapshot batchscripts☆140Updated 2 years ago
- SV detection from paired end reads mapping☆117Updated 5 years ago
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆157Updated 6 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆212Updated 8 months ago
- Finder of Somatic Fusion Genes in RNA-seq data☆145Updated last year
- Structural variation and indel detection by local assembly☆243Updated last week
- ABRA2☆92Updated 2 years ago
- This Snakemake pipeline implements the GATK best-practices workflow☆250Updated last year
- A structural variation pipeline for short-read sequencing☆183Updated this week
- A short tutorial on how to use RSEM☆136Updated 4 years ago
- Workflows for germline short variant discovery with GATK4☆134Updated 3 years ago
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆207Updated 3 weeks ago
- a lightweight bam file depth statistical tool☆150Updated 6 months ago
- FEELnc : FlExible Extraction of LncRNA☆87Updated 6 months ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆210Updated last week
- Relevant papers for CNV and SV approaches☆94Updated 4 months ago
- RNA-Seq analysis workflow☆104Updated 3 years ago
- Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads☆108Updated 2 years ago
- Fast and accurate gene fusion detection from RNA-Seq data☆234Updated this week
- Discovering known and novel miRNAs from small RNA sequencing data☆145Updated 6 months ago
- Annotation and Ranking of Structural Variation☆246Updated 2 weeks ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 5 years ago
- ☆113Updated last week
- Gene fusion detection and visualization☆122Updated 3 years ago
- ASCAT R package☆176Updated 3 months ago
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆215Updated 3 years ago
- The DevNet project on github stores the PacBio DevNet website.☆116Updated 6 years ago
- tools for adding mutations to existing .bam files, used for testing mutation callers☆239Updated 5 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆209Updated 4 years ago