Genomic variants - SNPs and INDELs detection using GATK4 spark based tools.
Version 1

Workflow Type: Common Workflow Language

Stable

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.

SEEK ID: https://workflowhub.eu/workflows/33?version=1

Inputs

ID	Name	Description	Type
sars_cov_2_reference_genome	n/a	n/a	File
sars_cov_2_reference_2bit_genome	n/a	n/a	File
rnaseq_left_reads	n/a	n/a	File
rnaseq_right_reads	n/a	n/a	File
sampleName	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
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