COVID-19: GATK4
Version 1

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Workflow Type: Galaxy

Stable

Detects SNPs and INDELs.

SEEK ID: https://workflowhub.eu/workflows/35?version=1

Inputs

ID	Name	Description	Type
bed_file	bed_file	runtime parameter for tool Filter SAM or BAM, output SAM or BAM	n/a
intervals	intervals	runtime parameter for tool SnpEff eff:	n/a
transcripts	transcripts	runtime parameter for tool SnpEff eff:	n/a

ID	Name	Description
0	List of Illumina accessions
1	Refrence genome
2	Reference genome annotation	COVID-19.gff
3	Illumina data	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4
4	SnpEff build:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
5	fastp: Trimmed Illumina Reads	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
6	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
7	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
8	Filter SAM or BAM, output SAM or BAM	toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1
9	Illumina filtered reads	toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
10	Bowtie2	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
11	AddOrReplaceReadGroups	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1
12	SortSam	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1
13	MarkDuplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
14	GATK4 Mutect2	toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.4.0+galaxy2
15	VcfAllelicPrimitives:	toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0
16	SnpEff eff:	Annotate variants. toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
17	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
18	Concatenate datasets	cat1

ID	Name	Description
list_paired	list_paired	n/a
output_collection	output_collection	n/a
output_collection_other	output_collection_other	n/a
log	log	n/a
snpeff_output	snpeff_output	n/a
output_paired_coll	output_paired_coll	n/a
report_html	report_html	n/a
report_json	report_json	n/a
bam_output	bam_output	n/a
stats	stats	n/a
html_report	html_report	n/a
output1	output1	n/a
forward	forward	n/a
reverse	reverse	n/a
output	output	n/a
mapping_stats	mapping_stats	n/a
outFile	outFile	n/a
outFile	outFile	n/a
metrics_file	metrics_file	n/a
outFile	outFile	n/a
output_vcf	output_vcf	n/a
out_file1	out_file1	n/a
snpeff_output	snpeff_output	n/a
statsFile	statsFile	n/a
output	output	n/a
out_file1	out_file1	n/a

Added/updated 2 files

Open master 27a22c7

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Views: 1264 Downloads: 51

Created: 18th Jun 2020 at 16:49

Last used: 8th Dec 2022 at 11:28