PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short read whole genome sequence data. GermlineStructuralV-nf identifies structural variant and copy number events from BAM files using Manta, Smoove, and TIDDIT. Variants are then merged using SURVIVOR, ...

Reads2Map

Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...

Reads2Map

Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...

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Somatic-ShortV @ NCI-Gadi is a variant calling pipeline that calls somatic short variants (SNPs and indels) from tumour and matched normal BAM files following GATK's Best Practice Workflow. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel. ...

Local Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

• Using hg38 human reference genome build
• Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the /data volume storage partition.
• Starting from short-read Illumina paired-end fastq ...

SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

• Using hg38 human reference genome build
• Running using HPC/SLURM scheduling. This repo was specifically tested on Pawsey Zeus machine, primarily running in the /scratch partition.
• Starting from short-read Illumina paired-end fastq files as input

Dependencies

The following versions have been ...

Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...