COVID-19: VARSCAN


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
COVID-19
Step 4: Faster Download and Extract Reads in FASTQ
List of SRA accession, one per line
Output dataset 'output' from step 1
Advanced Options:
Not available.
--split-3: write properly paired biological reads into different files and single reads in another file
True
Step 5: SnpEff build:
COVID-19
GFF
Output dataset 'output' from step 3
History
Output dataset 'output' from step 2
Standard
Step 6: fastp
Paired Collection
Output dataset 'list_paired' from step 4
Adapter Trimming Options:
False
Empty.
Empty.
Global trimming options:
Not available.
Not available.
Not available.
Not available.
Overrepresented Sequence Analysis:
False
Not available.
Filter Options:
Quality filtering options:
False
20
20
Not available.
Length filtering options:
False
50
Low complexity filtering options:
False
Not available.
Read Modification Options:
Automatic trimming for Illumina NextSeq/NovaSeq data
Not available.
Disable polyX trimming
UMI processing:
False
Empty.
Not available.
Empty.
Per read cutting by quality options:
False
False
Not available.
Not available.
Base correction by overlap analysis options:
False
Output Options:
True
True
Step 7: MultiQC
Results
Results 1
fastp
Output dataset 'report_json' from step 6
Empty.
Empty.
False
Step 8: Map with BWA-MEM
Use a built-in genome index
hg38
Paired Collection
Output dataset 'output_paired_coll' from step 6
Empty.
Do not set
1.Simple Illumina mode
Step 9: Filter SAM or BAM, output SAM or BAM
Output dataset 'bam_output' from step 8
Include header
Not available.
yes
The read is unmapped The mate is unmapped
Nothing selected.
Empty.
Empty.
select at runtime
False
Empty.
BAM (-b)
Step 10: Samtools fastx
Output dataset 'output1' from step 9
FASTQ
Not available.
False
False
READ1 READ2
False
Empty.
no
Nothing selected.
Nothing selected.
Nothing selected.
No
Step 11: Bowtie2
Paired-end
Output dataset 'forward' from step 10
Output dataset 'reverse' from step 10
False
False
No
Use a genome from the history and build index
Output dataset 'output' from step 2
Do not set
1: Default setting only
No, just use defaults
No
True
Step 12: Samtools sort
Output dataset 'output' from step 11
coordinate
Step 13: samtools mpileup
Use a genome from the history
Output dataset 'output1' from step 12
select at runtime
Basic
Default
Step 14: VarScan mpileup
Output dataset 'output_file_pu' from step 13
single nucleotide variation
8
2
15
0.01
0.75
0.99
no
Empty.
Step 15: VarScan mpileup
Output dataset 'output_file_pu' from step 13
insertions and deletions
8
2
15
0.01
0.75
0.99
no
Empty.
Step 16: VcfAllelicPrimitives:
Output dataset 'output' from step 14
False
Split primitives
200
False
False
Step 17: VcfAllelicPrimitives:
Output dataset 'output' from step 15
False
Split primitives
200
False
False
Step 18: SnpEff eff:
Output dataset 'out_file1' from step 16
VCF
VCF (only if input is VCF)
False
Custom snpEff database in your history
Output dataset 'snpeff_output' from step 5
Standard
5000 bases
2 bases
Use Defaults
Nothing selected.
select at runtime
select at runtime
Nothing selected.
No
Use default (based on input type)
Empty.
True
True
Step 19: SnpEff eff:
Output dataset 'out_file1' from step 17
VCF
VCF (only if input is VCF)
False
Custom snpEff database in your history
Output dataset 'snpeff_output' from step 5
Standard
5000 bases
2 bases
Use Defaults
Nothing selected.
select at runtime
select at runtime
Nothing selected.
No
Use default (based on input type)
Empty.
True
True
Step 20: SnpSift Extract Fields
Output dataset 'snpeff_output' from step 18
CHROM POS ID REF ALT
False
Empty.
Empty.
Step 21: SnpSift Extract Fields
Output dataset 'snpeff_output' from step 19
CHROM POS ID REF ALT
False
Empty.
Empty.
Step 22: Concatenate datasets
Output dataset 'output' from step 21
Datasets
Dataset 1
Output dataset 'output' from step 20