Dnanexus Apps and Scripts

• 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

• 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

• 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 *

• 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 GATK BaseRecalibrator and return the tables for use in HaplotypeCaller
• call_genotypes:
  • Obsolete, do not use; use geno_p instead. Calls GATK GenotypeGVCFs.
• call_hc:
  • Call GATK HaplotypeCaller and return gVCF files
• call_vqsr:
  • Calls GATK VariantRecalibrator and returns the files needed to apply the recalibration
• 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
  • Calls GATK CombineVariants to merge VCF files
• 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:
  • Calls GATK GenotypeGVCFs in parallel by chromosome
• merge_gvcfs:
  • Calls GATK CombineGVCFs
• plink_merge:
  • Merge PLINK bed/bim/fam files using PLINK 1.9
• select_variants: VCF QC
  • Calls GATK SelectVariants
• variant_annotator: VCF QC
  • Calls GATK VariantAnnotator
• vcf_annotate: Annotate VCF File
  • Use a variety of tools to annotate a sites-only VCF.
• vcf_concordance: VCF Concordance
  • Generate concordance metrics from VCF file(s) using GATK GenotypeConcordance. Not recommended for large files.
• 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:
  • Calls GATK ApplyRecalibration and GATK VariantFiltration to apply filters to VCF files.
• 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