Workflow Type: Galaxy
Open
Stable
Generic variant calling
A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:
- A genbank file with the reference genomes
- A collection of paired fastqsanger files
The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.
Workflow can be accessed directly on usegalaxy.org
The general idea of the workflow is:
Inputs
ID | Name | Description | Type |
---|---|---|---|
Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding | n/a |
GenBank genome | GenBank genome | n/a | n/a |
reads | reads | runtime parameter for tool Call variants | n/a |
reference_source | reference_source | runtime parameter for tool Call variants | n/a |
invcf | invcf | runtime parameter for tool Lofreq filter | n/a |
intervals | intervals | runtime parameter for tool SnpEff eff: | n/a |
transcripts | transcripts | runtime parameter for tool SnpEff eff: | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | Paired Collection | Illumina reads with fastqsanger encoding |
1 | GenBank genome | |
2 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
3 | SnpEff build: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 |
4 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
5 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 |
6 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
7 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
8 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 |
9 | Realign reads | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 |
10 | Insert indel qualities | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 |
11 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 |
12 | Lofreq filter | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 |
13 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
output_paired_coll | output_paired_coll | n/a | |
report_html | report_html | n/a | |
report_json | report_json | n/a | |
snpeff_output | snpeff_output | n/a | |
output_fasta | output_fasta | n/a | |
bam_output | bam_output | n/a | |
outputsam | outputsam | n/a | |
output | output | n/a | |
metrics_file | metrics_file | n/a | |
outFile | outFile | n/a | |
stats | stats | n/a | |
html_report | html_report | n/a | |
realigned | realigned | n/a | |
output | output | n/a | |
variants | variants | n/a | |
outvcf | outvcf | n/a | |
snpeff_output | snpeff_output | n/a | |
statsFile | statsFile | n/a |
Version History
Version 1 (earliest) Created 1st Jun 2022 at 13:46 by Anton Nekrutenko
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Wolfgang Maier
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Views: 155
Created: 1st Jun 2022 at 13:46
Last updated: 1st Jun 2022 at 16:51
Last used: 29th Jun 2022 at 04:21

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