Alternatives and similar repositories for AutoGVP:

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

• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated 11 months ago
• tf2 / CNest
  Copy Number Methods for Detection and Genome Wide Association Tests
  ☆22Updated 2 months ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆27Updated last year
• astrazeneca-cgr-publications / JARVIS
  JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes
  ☆22Updated 3 weeks ago
• macarthur-lab / tx_annotation
  Code associated with 2019 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation…
  ☆33Updated 2 years ago
• broadinstitute / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆25Updated 8 years ago
• gagneurlab / absplice
  ☆33Updated 4 months ago
• eyzhao / hrdetect-pipeline
  ☆34Updated 5 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 2 years ago
• PeeperLab / CopywriteR
  DNA copy number detection from off-target sequence data
  ☆30Updated 6 years ago
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆37Updated 3 years ago
• parklab / LiRA
  ☆18Updated 2 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 2 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 3 years ago
• WGLab / CancerVar
  Clinical interpretation of somatic mutations in cancer
  ☆44Updated 2 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆57Updated 11 months ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 4 years ago
• talkowski-lab / gnomad-sv-pipeline
  Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
  ☆36Updated 4 years ago
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆34Updated 3 years ago
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆49Updated last month
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆49Updated 2 years ago
• yuchaojiang / MARATHON
  Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
  ☆20Updated 5 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated last week
• parklab / ShatterSeek
  ☆65Updated last year
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆49Updated 5 months ago
• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 3 years ago