Find_Shared_Variants¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Phylogenetic Construction | Bacteria, Mycotics | PHB v2.0.0 | Yes | Set-level |
Find_Shared_Variants_PHB¶
Find_Shared_Variants_PHB is a workflow for concatenating the variant results produced by the Snippy_Variants_PHB workflow across multiple samples and reshaping the data to illustrate variants that are shared among multiple samples.
Find_Shared_Variants Workflow Diagram
Inputs¶
The primary intended input of the workflow is the snippy_variants_results output from Snippy_Variants_PHB or the theiaeuk_snippy_variants_results output of the TheiaEuk workflow. Variant results files from other tools may not be compatible at this time.
All variant data included in the sample set should be generated from aligning sequencing reads to the same reference genome. If variant data was generated using different reference genomes, shared variants cannot be identified and results will be less useful.
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| shared_variants_wf | concatenated_file_name | String | String of your choice to prefix output files | Required | |
| shared_variants_wf | samplenames | Array[String] | The samples to be included in the analysis | Required | |
| shared_variants_wf | variants_to_cat | Array[File] | The result file from the Snippy_Variants workflow | Required | |
| cat_variants | docker_image | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1" | Optional |
| shared_variants | cpu | Int | Number of CPUs to allocate to the task | 1 | Optional |
| shared_variants | disk_size | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| shared_variants | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-03-16" | Optional |
| shared_variants | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
| version_capture | docker | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | timezone | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | Optional |
Tasks¶
Concatenate Variants
Concatenate Variants Task¶
The cat_variants task concatenates variant data from multiple samples into a single file concatenated_variants. It is very similar to the cat_files task, but also adds a column to the output file that indicates the sample associated with each row of data.
The concatenated_variants file will be in the following format:
| samplename | CHROM | POS | TYPE | REF | ALT | EVIDENCE | FTYPE | STRAND | NT_POS | AA_POS | EFFECT | LOCUS_TAG | GENE | PRODUCT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sample1 | PEKT02000007 | 5224 | snp | C | G | G:21 C:0 | ||||||||
| sample2 | PEKT02000007 | 34112 | snp | C | G | G:32 C:0 | CDS | + | 153/1620 | 51/539 | missense_variant c.153C>G p.His51Gln | B9J08_002604 | hypothetical protein | |
| sample3 | PEKT02000007 | 34487 | snp | T | A | A:41 T:0 | CDS | + | 528/1620 | 176/539 | missense_variant c.528T>A p.Asn176Lys | B9J08_002604 | hypothetical protein |
Technical Details
| Links | |
|---|---|
| Task | /tasks/utilities/file_handling/task_cat_files.wdl |
| Software Source Code | task_cat_files.wdl |
Shared Variants Task
Shared Variants Task¶
The shared_variants task takes in the concatenated_variants output from the cat_variants task and reshapes the data so that variants are rows and samples are columns. For each variant, samples where the variant was detected are populated with a "1" and samples were either the variant was not detected or there was insufficient coverage to call variants are populated with a "0". The resulting table is available as the shared_variants_table output.
The shared_variants_table file will be in the following format:
| CHROM | POS | TYPE | REF | ALT | FTYPE | STRAND | NT_POS | AA_POS | EFFECT | LOCUS_TAG | GENE | PRODUCT | sample1 | sample2 | sample3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PEKT02000007 | 2693938 | snp | T | C | CDS | - | 1008/3000 | 336/999 | synonymous_variant c.1008A>G p.Lys336Lys | B9J08_003879 | NA | chitin synthase 1 | 1 | 1 | 0 |
| PEKT02000007 | 2529234 | snp | G | C | CDS | + | 282/336 | 94/111 | missense_variant c.282G>C p.Lys94Asn | B9J08_003804 | NA | cytochrome c | 1 | 1 | 1 |
| PEKT02000002 | 1043926 | snp | A | G | CDS | - | 542/1464 | 181/487 | missense_variant c.542T>C p.Ile181Thr | B9J08_000976 | NA | dihydrolipoyl dehydrogenase | 1 | 1 | 0 |
Technical Details
| Links | |
|---|---|
| Task | task_shared_variants.wdl |
| Software Source Code | task_shared_variants.wdl |
Outputs¶
The outputs of this workflow are the concatenated_variants file and the shared_variants_table file.
| Variable | Type | Description |
|---|---|---|
| concatenated_variants | File | The concatenated variants without presence/absence |
| shared_variants_analysis_date | String | The date the workflow was run |
| shared_variants_table | File | The shared variants table listing presence/absence for each mutation identified in the samples |
| shared_variants_version | String | The version of PHB the workflow is in |