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

Workflow Type: Common Workflow Language

Stable

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.

SEEK ID: https://workflowhub.eu/workflows/31?version=1

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

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