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Updated complex routines (Merge and Liftover)
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Graeme Ford committed Oct 10, 2023
1 parent bae0678 commit 7143dc2
Showing 1 changed file with 58 additions and 21 deletions.
79 changes: 58 additions & 21 deletions docs/02-workflow/02-analysis.md
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Original file line number Diff line number Diff line change
Expand Up @@ -56,20 +56,23 @@ Reference Genome Configuration
filterSampleRelatedness[[filterSampleRelatedness:\nremove a given list of]]
filterLocations[[filterLocations:\nTrim the dataset to one of\nthe studied regions]]
ifMultipleVcfs{If multiple\ndatasetsprovided}
subgraph multipleVcfProtocol [Multiple dataset protocol]
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
direction LR
multipleVcfProtocolStart(((Start)))
ifMergeRequired{Is a \nmerge needed?}
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
multipleVcfProtocolEnd(((End)))
multipleVcfProtocolStart --> ifMergeRequired
ifMergeRequired --> |yes| mergeDatasets --> multipleVcfProtocolEnd
ifMergeRequired --> |No| multipleVcfProtocolEnd
end
ifMultipleVcfs --> |yes| multipleVcfProtocol
ifMultipleVcfs --> |no| refFromFasta
multipleVcfProtocol --> refFromFasta --> chrFilter --> filterRequestedSamples --> filterVariantMissingness --> filterSampleMissingness --> calculateLinkageDisequilibrium
calculateLinkageDisequilibrium & filterSampleMissingness --> filterLinkageDisequilibrium
filterSampleMissingness & calculateLinkageDisequilibrium --> filterLinkageDisequilibrium
filterLinkageDisequilibrium --> calculateIdentityByDescent --> calculateSampleIds
Expand All @@ -89,9 +92,20 @@ Reference Genome Configuration
filter[[filter:\nRemove all variants except\nSNPs and INDELs]]
annotateKnown[[annotateKnown:\nAnnotate VCF against given\nreference VCF such as \n dbSNP]]
annotateUnknown[[annotateUnknown:\nName all un-annotated variants using \nstandardized naming conventions.]]
liftover[[liftover:\nPerform reference genome\nliftover]]
wipeInfo --> normalize --> sort --> filter --> annotateKnown --> annotateUnknown --> liftover
subgraph liftoverProtocol [Liftover]
direction LR
liftoverProtocolStart(((Start)))
liftover[[liftover:\nPerform reference genome\nliftover]]
liftoverProtocolEnd(((End)))
ifLiftoverRequired{Is a\nliftover\nrequired?}
liftoverProtocolStart --> ifLiftoverRequired
ifLiftoverRequired --> |yes| liftover --> liftoverProtocolEnd
ifLiftoverRequired --> |no| liftoverProtocolEnd
end
wipeInfo --> normalize --> sort --> filter --> annotateKnown --> annotateUnknown --> liftoverProtocol
end
subgraph PopulationStructureWorkflow [Population Structure Workflow]
plinkPca[[Plink_PCA:\nPerform a PLINK-2.0 PCA]]
Expand All @@ -104,12 +118,15 @@ Reference Genome Configuration
end
liftover --> ifMultipleVcfs
liftoverProtocol --> multipleVcfProtocol
END((Results))
plinkPca --> END
Admixture --> END
plinkPca --> END
reportFreq --> END
calculateIdentityByDescent --> END
calculateLinkageDisequilibrium --> END
```

</details>
Expand Down Expand Up @@ -227,13 +244,13 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filter[[filter:\nRemove all variants except\nSNPs and INDELs]]
filter[[filter:\nRemove all variant types\nexcept SNPs]]
```

<dl>
<dt>Function</dt>
<dd>
To remove all variant types except SNPs and INDELs</dd>
To remove all variant types except SNPs</dd>
<dt>Command</dt>
<dd><code>bcftools view -v snps -f PASS -O z -o {output.vcf} < {input.vcf}</code></dd>
<dt>Parameters</dt>
Expand Down Expand Up @@ -273,6 +290,8 @@ normalize[[normalize:\nNormalize all SNPs]]
<dt>Parameters</dt>
<dd>
<dl>
<dt><code>-a {input.annotations}</code></dt>
<dd>The VCF file that contains the desired annotations.</dd>
<dt><code>-c ID</code></dt>
<dd>Copy the <code>ID</code> column from the provided annotation VCF.</dd>
<dt><code>-O z</code></dt>
Expand Down Expand Up @@ -326,7 +345,17 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
liftover[[liftover:\nPerform reference genome\nliftover]]
subgraph liftoverProtocol [Liftover]
direction LR
liftoverProtocolStart(((Start)))
liftover[[liftover:\nPerform reference genome\nliftover]]
liftoverProtocolEnd(((End)))
ifLiftoverRequired{Is a\nliftover\nrequired?}
liftoverProtocolStart --> ifLiftoverRequired
ifLiftoverRequired --> |yes| liftover --> liftoverProtocolEnd
ifLiftoverRequired --> |no| liftoverProtocolEnd
end
```

<dl>
Expand Down Expand Up @@ -363,16 +392,24 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
subgraph multipleVcfProtocol [Multiple dataset protocol]
direction LR
multipleVcfProtocolStart(((Start)))
ifMergeRequired{Is a \nmerge needed?}
mergeDatasets[[mergeDatasets:\nMerge multiple incoming\ndatasets]]
multipleVcfProtocolEnd(((End)))
multipleVcfProtocolStart --> ifMergeRequired
ifMergeRequired --> |yes| mergeDatasets --> multipleVcfProtocolEnd
ifMergeRequired --> |No| multipleVcfProtocolEnd
end
```

> This rule only executes when multiple described datasets are detected.
This rule is responsible for merging multiple datasets into a single VCF file, suitable for collective analysis.
{: .normal }
> This rule only executes when multiple described datasets are detected. This rule is responsible for merging multiple datasets into a single VCF file, suitable for collective analysis.
<dl>
<dt>Function</dt>
<dd>
To perform reference-genome version liftovers.</dd>
<dd>To perform reference-genome version liftovers.</dd>
<dt>Command</dt>
<dd><code>bcftools merge -O z -o {output} {input.vcf}</code></dd>
<dt>Parameters</dt>
Expand Down Expand Up @@ -721,7 +758,7 @@ normalize[[normalize:\nNormalize all SNPs]]

```mermaid
flowchart TD
filterSampleRelatedness[[filterSampleRelatedness:\nremove a given list of]]
filterSampleRelatedness[[filterSampleRelatedness:\nremove a given list of samples\nbased on IBD results]]
```

<dl>
Expand Down

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