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 |
---|---|---|---|
GenBank genome | GenBank genome | n/a |
|
Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding |
|
Steps
ID | Name | Description |
---|---|---|
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 |
---|---|---|---|
fastp_pe | fastp_pe | n/a |
|
fastp_html_report | fastp_html_report | n/a |
|
SnpEff4.3 database for | SnpEff4.3 database for | n/a |
|
Fasta sequences for | Fasta sequences for | n/a |
|
Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) | Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) | n/a |
|
filtered_mapped_reads | filtered_mapped_reads | n/a |
|
mapped_reads_stats | mapped_reads_stats | n/a |
|
markduplicates_reads | markduplicates_reads | n/a |
|
markduplicates_stats | markduplicates_stats | n/a |
|
preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
|
realigned_deduplicated_filtered_mapped_reads | realigned_deduplicated_filtered_mapped_reads | n/a |
|
realigned_deduplicated_filtered_mapped_reads_with_indel_quals | realigned_deduplicated_filtered_mapped_reads_with_indel_quals | n/a |
|
called_variants | called_variants | n/a |
|
soft_filtered_variants | soft_filtered_variants | n/a |
|
_anonymous_output_1 | _anonymous_output_1 | n/a |
|
SnpEff eff: on input dataset(s) - stats | SnpEff eff: on input dataset(s) - stats | n/a |
|
Version History
Version 1 (earliest) Created 1st Jun 2022 at 13:46 by Anton Nekrutenko
Initial commit
Open
master
9738be7
Creators and Submitter
Creators
Not specifiedAdditional credit
Wolfgang Maier
Submitter
Discussion Channel
Activity
Views: 4300 Downloads: 478 Runs: 4
Created: 1st Jun 2022 at 13:46
Last updated: 1st Jun 2022 at 16:51
Attributions
None