h3abionet / h3agatk

Related projects ⓘ

Alternatives and complementary repositories for h3agatk

• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆54Updated 10 months ago
• 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…
  ☆50Updated 4 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆48Updated 5 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆32Updated 7 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆43Updated 5 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆64Updated 5 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆45Updated 6 years ago
• bgruening / galaxy-rna-workbench
  Galaxy RNA workbench
  ☆39Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆94Updated 3 years ago
• macarthur-lab / gnomad_browser
  gnomAD browser pre-ASHG 2018
  ☆33Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• KHP-Informatics / illumina-array-protocols
  processing illumina SNP arrays
  ☆19Updated 7 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆51Updated 7 years ago
• IARCbioinfo / gatk4-GenotypeGVCFs-nf
  Joint calling of gVCF, following GATK4 Best Practices
  ☆11Updated 5 years ago
• lh3 / tabtk
  Toolkit for processing TAB-delimited format
  ☆59Updated last month
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆76Updated 4 years ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆66Updated last year
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆74Updated last year
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 2 weeks ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆70Updated 2 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆37Updated 3 years ago
• gatk-workflows / five-dollar-genome-analysis-pipeline
  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  ☆57Updated 4 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆31Updated 2 years ago
• GenomiqueENS / dockerfiles
  ☆82Updated 2 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆49Updated 2 years ago