Workflow Type: Common Workflow Language
Open
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 GATK4.
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 |
|
sars_cov_2_reference_2bit_genome | n/a | n/a |
|
rnaseq_left_reads | n/a | n/a |
|
rnaseq_right_reads | n/a | n/a |
|
sampleName | n/a | n/a |
|
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 |
create_sequence_dictionary | n/a | n/a |
update_read_group | n/a | n/a |
sort_sam | n/a | n/a |
mark_duplicates | n/a | n/a |
split_alignments | n/a | n/a |
index_split_alignments | n/a | n/a |
call_plausible_haplotypes_and_detect_variants | n/a | n/a |
filer_out_low_quality_variants | n/a | n/a |
select_indels | n/a | n/a |
select_snps | n/a | n/a |
Outputs
ID | Name | Description | Type |
---|---|---|---|
indels | n/a | n/a |
|
snps | n/a | n/a |
|
Version History
Version 1 (earliest) Created 17th Jun 2020 at 07:38 by Ambarish Kumar
Added/updated 2 files
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