PapenfussLab / StructuralVariantAnnotation

Related projects ⓘ

Alternatives and complementary repositories for StructuralVariantAnnotation

• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆44Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆66Updated 2 months ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆48Updated 3 months ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆44Updated last year
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated 8 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
• cc2qe / vawk
  An awk-like VCF parser
  ☆54Updated 10 months ago
• nhansen / SVanalyzer
  Tools for the analysis of structural variation in genomes
  ☆77Updated 7 months ago
• talkowski-lab / gnomad-sv-pipeline
  Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
  ☆36Updated 4 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆77Updated 9 months ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated 3 weeks ago
• zd1 / telseq
  A software for calculating telomere length
  ☆67Updated 6 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆69Updated 4 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 5 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 4 months ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆101Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆94Updated 3 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆74Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆28Updated 6 years ago
• ryanlayer / stix
  Structural Variant Index
  ☆70Updated this week
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆31Updated 2 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆98Updated this week
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆82Updated last week
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆92Updated 7 months ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago