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
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Views: 655   Downloads: 48

Created: 17th Jun 2020 at 07:24

Last used: 6th Dec 2021 at 14:43

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

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