Workflow Type: Common Workflow Language
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Stable
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 |
|
rnaseq_left_reads | n/a | n/a |
|
rnaseq_right_reads | n/a | n/a |
|
sample_name | n/a | n/a |
|
Steps
ID | Name | Description |
---|---|---|
index_reference_genome_with_bowtie2 | n/a | n/a |
align_rnaseq_reads_to_genome | n/a | n/a |
index_reference_genome_with_samtools | n/a | n/a |
sam_to_bam_conversion_using_samtools_view | n/a | n/a |
sort_alignment_files_using_samtools_sort | n/a | n/a |
index_bam_files_using_samtools_index | n/a | n/a |
mpileup_generation_using_samtools_mpileup | n/a | n/a |
snp_calling_using_mpileup2snp | n/a | n/a |
indel_calling_using_mpileup2indel | n/a | n/a |
Outputs
ID | Name | Description | Type |
---|---|---|---|
snps | n/a | n/a |
|
indels | n/a | n/a |
|
Version History
Version 1 (earliest) Created 17th Jun 2020 at 07:24 by Ambarish Kumar
Added/updated 2 files
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Created: 17th Jun 2020 at 07:24
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