Creator: Ambarish Kumar
Submitter: Ambarish Kumar
External LinkDetects SNPs and short INDELs.
Creator: Ambarish Kumar
Submitter: Ambarish Kumar
ONT Artificial Deletion Filter-Delter
A tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries.
Requirements
The tool has been tested on Ubuntu 20.04 with 256GB RAM, 64 CPU cores and a NVIDIA GPU with 48GB RAM. The minimal requirements should be >= 64GB RAM and a NVIDIA GPU with >= 8GB RAM. Other operating systems like Windows or Mac were not tested.
ONT softwares like Guppy, ...
Parabricks-Genomics-nf is a GPU-enabled pipeline for alignment and germline short variant calling for short read sequencing data. The pipeline utilises NVIDIA's Clara Parabricks toolkit to dramatically speed up the execution of best practice bioinformatics tools. Currently, this pipeline is configured specifically for NCI's Gadi HPC.
NVIDIA's Clara Parabricks can deliver a significant ...
This is a Nextflow implementaion of the GATK Somatic Short Variant Calling workflow. This workflow can be used to discover somatic short variants (SNVs and indels) from tumour and matched normal BAM files following GATK's Best Practices Workflow. The workflowis currently optimised to run efficiently and at scale on the National Compute Infrastructure, Gadi.
Type: Nextflow
Creators: Nandan Deshpande, Tracy Chew, Cali Willet, Georgina Samaha
Submitter: Georgina Samaha
Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...
DownloadSomatic-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. ...
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
/scratchpartition. - Starting from short-read Illumina paired-end fastq files as input
Dependencies
The following versions have been ...
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
/datavolume storage partition. - Starting from short-read Illumina paired-end fastq ...
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 ...
Type: Shell Script
Creators: Rosemarie Sadsad, Georgina Samaha, Tracy Chew, Cali Willet
Submitter: Tracy Chew
Detects SNPs and INDELs using VARSCAN2.
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using SAMTools.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using VARSCAN.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
