Alternatives and similar repositories for breakseq2

Users that are interested in breakseq2 are comparing it to the libraries listed below

• AstraZeneca-NGS / simple_sv_annotation
  Simplify snpEff annotations for interesting cases
  ☆22Updated 6 years ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 4 years ago
• lganel / SVScore
  Prioritize structural variants based on CADD scores
  ☆29Updated 5 years ago
• lh3 / sgdp-fermi
  FermiKit small variant calls for public SGDP samples
  ☆17Updated 8 years ago
• ssadedin / ximmer
  Ximmer is a system for CNV calling on exome and targeted genomic sequencing
  ☆19Updated last week
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆31Updated last month
• DecodeGenetics / popSTR
  PopSTR - A Population based microsatellite genotyper
  ☆33Updated last year
• jcarrotzhang / LoLoPicker
  picking up low allelic-fraction, somatic variants from tumor samples
  ☆14Updated 7 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆23Updated 2 months ago
• quinlan-lab / ccrhtml
  A small repo for storing the code for making the files and html for CCRs.
  ☆22Updated 5 years ago
• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 4 years ago
• ryanlayer / svv
  Stupid Simple Structural Variant View
  ☆25Updated 8 years ago
• lh3 / rtgeval
  Wrapper for RTG's vcfeval; DEPRECATED!
  ☆21Updated 9 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 6 years ago
• brentp / gsort
  sort genomic data
  ☆36Updated 5 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• brentp / excord
  extract SV signal from a BAM
  ☆11Updated 7 years ago
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆38Updated 6 months ago
• lh3 / unicall
  A wrapper for calling small variants from human germline high-coverage single-sample Illumina data
  ☆14Updated 6 years ago
• lh3 / pre-pe
  Preprocessing paired-end reads produced with experiment-specific protocols
  ☆32Updated 7 years ago
• applevir / STEAK
  Specific Transposable Element Aligner (HERV-K)
  ☆16Updated 6 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago