Genomic variants - SNPs and INDELs detection using VARSCAN2.
Version 1

Workflow Type: Common Workflow Language
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
  • 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 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
  • File
indels n/a n/a
  • File

Version History

Version 1 (earliest) Created 17th Jun 2020 at 07:24 by Ambarish Kumar

Added/updated 2 files


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Views: 1009   Downloads: 56

Created: 17th Jun 2020 at 07:24

Last used: 26th Jun 2022 at 10:01

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