Alternatives and similar repositories for chanjo:

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

• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 4 years ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 4 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago
• brentp / geneimpacts
  prioritize effects of variant annotations from VEP, SnpEff, et al.
  ☆33Updated 4 months ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago
• robinandeer / puzzle
  Variant caller GUI + genetic disease analysis
  ☆22Updated 4 years ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆32Updated last year
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 3 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 5 years ago
• brentp / bigly
  a pileup library that embraces the huge
  ☆42Updated 4 years ago
• Yandell-Lab / VVP-pub
  VVP (VAAST Variant Prioritizer) rapidly prioritizes genetic variants
  ☆19Updated 7 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• pughlab / VisCap
  VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…
  ☆22Updated 5 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• dillonl / graphite
  Graphite - Graph-based variant adjudication
  ☆28Updated 4 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• AstraZeneca-NGS / simple_sv_annotation
  Simplify snpEff annotations for interesting cases
  ☆21Updated 6 years ago
• vibansal / hapcut
  program for haplotype phasing from sequence reads and related tools
  ☆25Updated 6 years ago
• dnil / rhocall
  Call regions of homozygosity and make tentative UPD calls
  ☆11Updated 4 months ago
• Clinical-Genomics / stranger
  Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
  ☆32Updated last month
• 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
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆31Updated 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
• 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
• sequencing / NxTrim
  Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.
  ☆54Updated 6 years ago
• cancerit / cgpBigWig
  BigWig manpulation tools using libBigWig and htslib
  ☆29Updated 8 months ago
• cauyrd / ScanIndel
  The integrated pipeline for Indel detection
  ☆17Updated 6 years ago