Genomic variants - SNPs and INDELs detection using GATK4. 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 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 | File |
| rnaseq_left_reads | n/a | n/a | File |
| rnaseq_right_reads | n/a | n/a | File |
| indices_folder | n/a | n/a | Directory |
Steps
| ID | Name | Description |
|---|---|---|
| index_reference_genome_with_bowtie2 | ||
| align_rnaseq_reads_to_genome | ||
| index_reference_genome_with_samtools | ||
| create_sequence_dictionary | ||
| update_read_group | ||
| mark_duplicates | ||
| split_alignments | ||
| index_split_alignments | ||
| call_plausible_haplotypes_and_detect_variants | ||
| filer_out_low_quality_variants | ||
| select_indels | ||
| select_snps |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| indels | n/a | n/a | File |
| snps | n/a | n/a | File |
Creators and Submitter
License
Activity
Views: 80 Downloads: 6
Created: 17th Jun 2020 at 07:11
Last used: 11th Aug 2020 at 18:35
AttributionsNone
Related items
CWL workflows related to virus genomics with focus on SARS-CoV-2.
Space: COVID-19 Biohackathon
Public web page: https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2
External Link