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 SAMTools.
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 | ||
snp_generation_using_bcftools | ||
indel_generation_using_bcftools |
Outputs
ID | Name | Description | Type |
---|---|---|---|
snp | n/a | n/a | File |
indel | n/a | n/a | File |