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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 |

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Views: 242 Downloads: 22
Created: 17th Jun 2020 at 07:11
Last used: 18th Jan 2021 at 21:20

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