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dnanexus_congenica_upload

DNAnexus app for uploading samples to the Congenica analysis platform

dnanexus_convert_to_rpkm_bedfile

SUPERSEDED BY EXOME DEPTH. DNANexus app creating bedfiles suitable for use with the DNA nexus RPKM app

dnanexus_coverage_uniformity_report

DNA Nexus App to calculate uniformity of coverage across multiple samples from Sambamba raw output

dnanexus_duty_csv

DNAnexus implementation of duty_csv. To be used in conjunction with process_duty_csv

dnanexus_ed_cnv_calling

Performs CNV calling using ExomeDepth.

dnanexus_ed_readcount_analysis

This app calculates the readcount for a batch of samples for CNV calling using ExomeDepth.

dnanexus_fastqc

DNAnexus app generating a QC report on reads data

dnanexus_fh_prs

Calculation of polygenic risk score (PRS) for FH samples

dnanexus_filter_vcf_with_bedfile

DNAnexus app to filter variants after variant calling using a BED file

dnanexus_gatk_diagnose_targets

dnanexus_gatk_genotypegvcfs

dnanexus_gatk_haplotypecaller

dnanexus_gatk_preprocessing

Performs GATK preprocessing steps as per GATK best practice

dnanexus_gatk_variantannotator

dnanexus_gatk_variant_calling

OBSOLETE: REPLACED BY SENTIEON. DNAnexus app performing variant calling. For use once when you have mapped exome reads to the human genome, and want to identify variants (SNPs and indels) using the GATK 3.x best practices method

dnanexus_happy

DNAnexus app comparing a query VCF to a truth VCF to calculate performance metrics including sensitivity and precision using hap.py and vcfeval

dnanexus_integrity_test

Tests the integrity of the DNANexus platform

dnanexus_lofreq

DNANexus app to run Lofreq variant caller

dnanexus_minimap2_nanopore

dnanexus_mokaamp_workflow

NO LONGER IN PROD USE. Workflow description of DNANexus workflow MokaAMP

dnanexus_mokabed

Utilises the moka-guys/mokabed code to generate BED files

dnanexus_mokacan_workflow

Workflow description of DNANexus workflow MokaCAN

dnanexus_mokaonc_workflow

Workflow description of DNANexus workflow MokaONC. Replaced by MokaAMP

dnanexus_mokapicard

DNAnexus app using Picard Tools to generate quality-control (QC) statistics from mapped/aligned reads

dnanexus_mokapipe_workflow

Workflow description of DNANexus workflow GATK3.5

dnanexus_mokasnp_workflow

OBSOLETE: Workflow description of DNANexus workflow 'SNP Genotyping' (genotypes a set of SNPs to be uploaded to the sample matching service for the GMS WGS)

dnanexus_mokavendor

dnanexus_mokawes_workflow

OBSOLETE: Workflow description of DNANexus workflow MokaWES

dnanexus_mpileup

dnanexus_mpileup_coverage

To be used for SCIP. DNAnexus app calculating whether each amplicon is covered sufficiently - represents the coverage available to varscan. Runs script from moka-guys/mpileup_coverage