/dnanexus

Primary LanguageC++

DNAnexus

Dnanexus Apps and Scripts

applets

  • binning_step0: BioBin Pipeline
  • biobin_pipeline
  • binning_step1: BioBin Pipeline
  • biobin_pipeline
  • binning_step2: BioBin Pipeline
  • biobin_pipeline
  • binning_step3: BioBin Pipeline
  • biobin_pipeline
  • impute2_group_join: Impute2_group_join
  • This app can be used to merge multiple imputed impute2 files
  • plato_biobin: PLATO BioBin Regression Analysis
  • PLATO_BioBin
  • vcf_batch: VCF Batch effect tester
  • vcf_batch

apps

  • association_result_annotation: Annotate GWAS, PheWAS Assocaitions
  • association_result_annotation
  • biobin:
  • This app runs the latest development build of the rare variant binning tool BioBin.
  • generate_phenotype_matrix: Generate Phenotype Matrix
  • generate_phenotype_matrix
  • genotype_case_control: Generate Case/Control by Genotype
  • App provides case and control number by each genotype
  • impute2: imputation
  • This will perfrom imputation using Impute2
  • impute2_to_plink: Impute2 To PLINK
  • Convert Impute2 file to PLINK files
  • plato_single_variant: PLATO - Single Variant Analysis
  • Apps allows you to run single variant association testing against single phenotype (GWAS) or multiple phenotype (PheWAS) test
  • rl_sleeper_app: sleeper
  • This App provides some useful tools when working with data in DNANexus. This App is designed to be run on the command line with "dx run --ssh RL_Sleeper_App" in the project that you have data that you want to explore (use "dx select" to switch projects as needed).
  • shapeit2: SHAPEIT2
  • This app do phasing using SHAPEIT2
  • strand_align: Strand Align
  • Strand Align prior to phasing
  • vcf_annotation_formatter:
  • Extracts and reformats VCF annotations (CLINVAR, dbNSFP, SIFT, SNPEff)
  • QC_apps subfolder:
    • drop_marker_sample: Drop Markers and/or Samples (PLINK)
      • drop_marker_sample
  • drop_relateds: Relatedness Filter (IBD)
    • drop_relateds
  • extract_marker_sample: Drop Markers and/or Samples (PLINK)"
    • extract_marker_sample
  • maf_filter: Marker MAF Rate Filter (PLINK)
    • maf_filter
  • marker_call_filter: Marker Call Rate Filter (PLINK)
    • marker_call_filter
  • missing_summary: Missingness Summary (PLINK)
    • Returns missingness rate by sample
  • pca: Principal Component Analysis using SMARTPCA
    • pca
  • sample_call_filter: Sample Call Rate Filter (PLINK)
    • sample_call_filter

scripts

  • cat_vcf.py *
  • download_intervals.py *
  • download_part.py *
  • estimate_size.py *
  • interval_pad.py
    • This reads a bed file from standard input, pads the intervals, sorts and then outputs the intervals guranteed to be non-overlapping
  • update_applet.sh *

sequencing

  • bcftools_view:
    • Calls "bcftools view". Still in experimental stages.
  • calc_ibd:
    • Calculates a pairwise IBD estimate from either VCF or PLINK files using PLINK 1.9.
  • call_bqsr: Base Quality Score Recalibration
  • call_genotypes:
    • Obsolete, do not use; use geno_p instead. Calls GATK GenotypeGVCFs.
  • call_hc:
  • call_vqsr:
  • cat_variants: combine_variants
    • Combines non-overlapping VCF files with the same subjects. A reimplementation of GATK CatVariants (GATK CatVariants available upon request)
  • combine_variants: combine_variants
  • gen_ancestry:
    • Determine Ancestry from PCA. Uses an eigenvector file and training dataset listing known ancestries. Runs QDA to determine posterior ancestries for all samples, even those in the training set.
  • gen_related_todrop:
    • Uses a PLINK IBD file to determine the minimal set of samples to drop in order to generate an unrelated sample set. Uses a minimum vertex cut algorithm of the related samples to get
  • geno_p:
  • merge_gvcfs:
  • plink_merge:
    • Merge PLINK bed/bim/fam files using PLINK 1.9
  • select_variants: VCF QC
  • variant_annotator: VCF QC
  • vcf_annotate: Annotate VCF File
    • Use a variety of tools to annotate a sites-only VCF.
  • vcf_concordance: VCF Concordance
  • vcf_gen_lof:
    • Subset a VCF from vcf_annotate based on the given annotations to get a sites-only VCF of loss-of-function variants.
  • vcf_pca:
    • Uses PLINK 1.9 and eigenstrat 6.0 to calculate principal components from VCF or PLINK bed/bim/fam files.
  • vcf_qc:
  • vcf_query:
    • Calls "bcftools query" to extract annotations from the VCF file. Used in the stripping of files for MEGAbase
  • vcf_sitesonly: VCF QC
    • Generates a sites-only file from full VCF files.
  • vcf_slice: Slice VCF File(s)
    • Return a small section of a VCF file (similar to tabix). For large output, many small regions, or subsetting samples, use subset_vcf instead.
  • vcf_summary: VCF Summary Statistics
    • Generate summary statistics for a VCF file (by sample and by variant)
  • vcf_to_plink:
    • Uses PLINK 1.9 to convert VCF files to PLINK bed/bim/fam files