Alternatives and similar repositories for gatk4-somatic-snvs-indels

Users that are interested in gatk4-somatic-snvs-indels are comparing it to the libraries listed below

• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 8 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 8 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆57Updated 5 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆112Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• bioinform / rnacocktail
  ☆89Updated 5 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆99Updated 3 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• raerose01 / deconstructSigs
  deconstructSigs
  ☆144Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆135Updated last year
• OSU-SRLab / MANTIS
  Microsatellite Analysis for Normal-Tumor InStability
  ☆75Updated 3 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆141Updated 4 months ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• csf-ngs / fastqc
  csf fork of fastqc for usage on selected reads of unaligned bam file
  ☆48Updated 12 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago