snakemake-workflows / dna-seq-gatk-variant-callingLinks
This Snakemake pipeline implements the GATK best-practices workflow
☆260Updated 2 years ago
Alternatives and similar repositories for dna-seq-gatk-variant-calling
Users that are interested in dna-seq-gatk-variant-calling are comparing it to the libraries listed below
Sorting:
- Count bases in BAM/CRAM files☆319Updated 3 years ago
- Fast and accurate gene fusion detection from RNA-Seq data☆253Updated last month
- Plot structural variant signals from many BAMs and CRAMs☆555Updated last year
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆274Updated 2 years ago
- Full-Length Alternative Isoform analysis of RNA☆240Updated this week
- parallel fastq-dump wrapper☆299Updated 2 years ago
- Documentation for the ANNOVAR software☆245Updated 3 months ago
- RNA-seq workflow using STAR and DESeq2☆346Updated 2 months ago
- A package for including transposable elements in differential enrichment analysis of sequencing datasets.☆267Updated last week
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆165Updated 2 years ago
- SUPPA: Fast quantification of splicing and differential splicing☆284Updated last week
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆393Updated 2 weeks ago
- Annotation and Ranking of Structural Variation☆267Updated last month
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆243Updated 4 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆402Updated 3 months ago
- PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.☆283Updated 9 months ago
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆226Updated 4 months ago
- A collection of scripts and notes related to genomics and bioinformatics☆217Updated last week
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆230Updated 3 years ago
- TransDecoder source☆298Updated last month
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel☆181Updated this week
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆250Updated 4 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆328Updated 5 months ago
- Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.☆280Updated 3 months ago
- Quick mining and visualization of NGS data by integrating genomic databases☆268Updated 2 years ago
- VarDict☆200Updated last year
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆244Updated this week
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆244Updated 2 years ago
- STAR-Fusion codebase☆245Updated last month
- ATAC-seq peak-calling and QC analysis pipeline☆213Updated last week