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_marker_sample: Drop Markers and/or Samples (PLINK)
- 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
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