Alternatives and similar repositories for checkVCF

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

• biocore-ntnu / snpflip
  Report reverse and ambiguous strand SNPs in GWAS data
  ☆33Updated 6 years ago
• CshlSiepelLab / LINSIGHT
  ☆26Updated last month
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆34Updated 8 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.
  ☆49Updated 6 years ago
• freeseek / gwaspipeline
  ☆40Updated 7 years ago
• statgen / locuszoom-standalone
  Create regional association plots from GWAS or meta-analysis
  ☆61Updated 5 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• sritchie73 / liftOverPlink
  A wrapper for liftOver for converting plink genotype data between different genome reference builds
  ☆52Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 4 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆41Updated 7 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• broadinstitute / oncotator
  ☆68Updated 3 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 4 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆41Updated 3 years ago
• joepickrell / fgwas
  Functional genomics and genome-wide association studies
  ☆67Updated 6 years ago
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆37Updated 4 years ago
• daler / trackhub
  create, manage, and upload track hubs for use in the UCSC genome browser
  ☆54Updated last year
• 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…
  ☆53Updated 4 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• macarthur-lab / exac_2015
  Companion repo for ExAC paper, 2015
  ☆33Updated 8 years ago
• BIMSBbioinfo / genomation
  R package for genomic feature analysis and visualization
  ☆79Updated 3 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 8 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• UW-GAC / analysis_pipeline
  TOPMed analysis pipeline
  ☆52Updated last year
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• grst / snakemake_nextflow_wdl
  simple comparison of snakemake, nextflow and cromwell/wdl
  ☆49Updated 4 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆49Updated 11 months ago