Genomic variants - SNPs and INDELs detection using VARSCAN2. Version 1
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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.
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
License
Activity
Views: 257 Downloads: 27
Created: 17th Jun 2020 at 07:24
Last used: 19th Jan 2021 at 20:12
AttributionsNone
Related items
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
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