COVID-19: VARSCAN
Version 1

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Detects SNPs and INDELs using VARSCAN2.

SEEK ID: https://workflowhub.eu/workflows/36?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
intervals	intervals	runtime parameter for tool SnpEff eff:	n/a
transcripts	transcripts	runtime parameter for tool SnpEff eff:	n/a
input1	input1	runtime parameter for tool Concatenate datasets	n/a

Steps

ID	Name	Description
0	List of Illumina accessions
1	Reference genome
2	Reference genome annotation	COVID-19
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	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
7	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
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	Samtools sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3
12	samtools mpileup	toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4
13	VarScan mpileup	toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1
14	VarScan mpileup	toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1
15	VcfAllelicPrimitives:	toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0
16	VcfAllelicPrimitives:	toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0
17	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
18	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
19	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
20	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
21	Concatenate datasets	cat1

Outputs

ID	Name	Description	Type
list_paired	list_paired	n/a	input
output_collection	output_collection	n/a	input
output_collection_other	output_collection_other	n/a	input
log	log	n/a	txt
snpeff_output	snpeff_output	n/a	snpeffdb
output_paired_coll	output_paired_coll	n/a	input
report_html	report_html	n/a	html
report_json	report_json	n/a	json
stats	stats	n/a	input
html_report	html_report	n/a	html
bam_output	bam_output	n/a	bam
output1	output1	n/a	sam
forward	forward	n/a	fasta
reverse	reverse	n/a	fasta
output	output	n/a	bam
mapping_stats	mapping_stats	n/a	txt
output1	output1	n/a	bam
output_file_pu	output_file_pu	n/a	pileup
output	output	n/a	vcf
output	output	n/a	vcf
out_file1	out_file1	n/a	vcf
out_file1	out_file1	n/a	vcf
snpeff_output	snpeff_output	n/a	vcf
statsFile	statsFile	n/a	html
snpeff_output	snpeff_output	n/a	vcf
statsFile	statsFile	n/a	html
output	output	n/a	tabular
output	output	n/a	tabular
out_file1	out_file1	n/a	input

Creators and Submitter

Creators

Not specified

Submitter

Ambarish Kumar

License

Apache Software License 2.0

Activity

Views: 436 Downloads: 26

Created: 18th Jun 2020 at 23:57

Last used: 3rd Mar 2021 at 19:58

Version History

Version 1 Created 18th Jun 2020 at 23:57 by Ambarish Kumar

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COVID-19: VARSCAN Version 1