Workflow Type: Galaxy
Frozen
Workflow for variant analysis against a reference genome in GenBank format
Inputs
ID | Name | Description | Type |
---|---|---|---|
Annotation GTF | Annotation GTF | GTF with gene annotation, will be used for annotating variants |
|
Genome fasta | Genome fasta | Fasta file to use as reference for variant calling |
|
Paired Collection | Paired Collection | Illumina reads with fastqsanger encoding |
|
Steps
ID | Name | Description |
---|---|---|
3 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
4 | SnpEff build: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6 |
5 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
6 | Samtools view | Retains alignments if read is paired and mapped in proper orientation toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1 |
7 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
8 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
9 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
10 | Realign reads | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 |
11 | Call variants | toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3 |
12 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
13 | SnpEff eff: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 |
14 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
15 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
fastp html report | fastp html report | n/a |
|
SnpEff4.3 database | SnpEff4.3 database | n/a |
|
Preprocessing and mapping reports | Preprocessing and mapping reports | n/a |
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SnpEff variants | SnpEff variants | n/a |
|
SnpEff eff reports | SnpEff eff reports | n/a |
|
Annotated Variants | Annotated Variants | n/a |
|
Version History
v0.1 (earliest) Created 30th Oct 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
963ebf4