COVID-19: GATK4

ID	Name	Description	Type
List of Illumina accessions	List of Illumina accessions	n/a	File
Reference genome annotation	Reference genome annotation	COVID-19.gff	File
Refrence genome	Refrence genome	n/a	File

ID	Name	Description
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	Type
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
_anonymous_output_12	_anonymous_output_12	n/a	File
_anonymous_output_13	_anonymous_output_13	n/a	File
_anonymous_output_14	_anonymous_output_14	n/a	File
_anonymous_output_15	_anonymous_output_15	n/a	File
_anonymous_output_16	_anonymous_output_16	n/a	File
_anonymous_output_17	_anonymous_output_17	n/a	File
_anonymous_output_18	_anonymous_output_18	n/a	File
_anonymous_output_19	_anonymous_output_19	n/a	File
_anonymous_output_20	_anonymous_output_20	n/a	File
VCF	VCF	n/a	File
_anonymous_output_21	_anonymous_output_21	n/a	File
_anonymous_output_22	_anonymous_output_22	n/a	File
_anonymous_output_23	_anonymous_output_23	n/a	File
_anonymous_output_24	_anonymous_output_24	n/a	File
_anonymous_output_25	_anonymous_output_25	n/a	File

COVID-19: GATK4
Version 1