moka-guys Goto Github PK
Name: MokaGuys
Type: Organization
Name: MokaGuys
Type: Organization
DNAnexus app for uploading samples to the Congenica analysis platform
SUPERSEDED BY EXOME DEPTH. DNANexus app creating bedfiles suitable for use with the DNA nexus RPKM app
DNA Nexus App to calculate uniformity of coverage across multiple samples from Sambamba raw output
DNAnexus implementation of duty_csv. To be used in conjunction with process_duty_csv
Performs CNV calling using ExomeDepth.
This app calculates the readcount for a batch of samples for CNV calling using ExomeDepth.
DNAnexus app generating a QC report on reads data
Calculation of polygenic risk score (PRS) for FH samples
DNAnexus app to filter variants after variant calling using a BED file
Performs GATK preprocessing steps as per GATK best practice
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 app comparing a query VCF to a truth VCF to calculate performance metrics including sensitivity and precision using hap.py and vcfeval
Tests the integrity of the DNANexus platform
DNANexus app to run Lofreq variant caller
NO LONGER IN PROD USE. Workflow description of DNANexus workflow MokaAMP
Utilises the moka-guys/mokabed code to generate BED files
Workflow description of DNANexus workflow MokaCAN
Workflow description of DNANexus workflow MokaONC. Replaced by MokaAMP
DNAnexus app using Picard Tools to generate quality-control (QC) statistics from mapped/aligned reads
Workflow description of DNANexus workflow GATK3.5
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)
OBSOLETE: Workflow description of DNANexus workflow MokaWES
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
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