Genomic variants - SNPs and INDELs detection using VARSCAN2. Version 1
View on GitHub
Download RO-CrateAuthor: 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.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| sars_cov_2_reference_genome | n/a | n/a | File |
| rnaseq_left_reads | n/a | n/a | File |
| rnaseq_right_reads | n/a | n/a | File |
| sample_name | n/a | n/a | string |
Steps
| ID | Name | Description |
|---|---|---|
| index_reference_genome_with_bowtie2 | ||
| align_rnaseq_reads_to_genome | ||
| index_reference_genome_with_samtools | ||
| sam_to_bam_conversion_using_samtools_view | ||
| sort_alignment_files_using_samtools_sort | ||
| index_bam_files_using_samtools_index | ||
| mpileup_generation_using_samtools_mpileup | ||
| snp_calling_using_mpileup2snp | ||
| indel_calling_using_mpileup2indel |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| snps | n/a | n/a | File |
| indels | n/a | n/a | File |
Creators and Submitter
Views: 655 Downloads: 48
Created: 17th Jun 2020 at 07:24
Last used: 6th Dec 2021 at 14:43
AttributionsNone
Version History
Version 1 Created 17th Jun 2020 at 07:24 by Ambarish Kumar
No revision comments
Related items
The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone ...
Teams: Connor Lab, GalaxyProject SARS-CoV-2, InSaFLU, nf-core viralrecon, CWL workflow SARS-CoV-2, V-Pipe, Test team
Web page: https://github.com/virtual-biohackathons/covid-19-bh20
CWL workflows related to virus genomics with focus on SARS-CoV-2.
Space: COVID-19 Biohackathon
Public web page: https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2
External Link
