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

Workflow Type: Common Workflow Language

Stable

This is a proposed standard operating procedure for genomic variant detection using SAMTools.

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/34?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
snp_generation_using_bcftools	n/a	n/a
indel_generation_using_bcftools	n/a	n/a

ID	Name	Description	Type
snp	n/a	n/a	File
indel	n/a	n/a	File

Added/updated 2 files

Open master 64d0fd2

Creators and Submitter

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License

Activity

Views: 1400 Downloads: 81

Created: 17th Jun 2020 at 08:41

Last updated: 27th Jun 2020 at 02:27

Last used: 30th Sep 2022 at 10:48