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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 |

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Views: 257 Downloads: 27
Created: 17th Jun 2020 at 07:24
Last used: 19th Jan 2021 at 20:12

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