Add xml workflow

docs/analysis-workflows/analysis-overview.md

@@ -13,6 +13,7 @@ The ARGO Data Platform will accept a wide range of datatypes, including:
 - DNA Methylation data
 - Transcriptomic data
 - Proteomic data
+- Variant calling data (in XML format)
 - Slide images
 
 Pipelines, and the individual analysis workflows that they are constructed from, have been developed by the DCC Bioinformatics team based on established, best community practices.

docs/analysis-workflows/xml-ingestion.md

@@ -0,0 +1,29 @@
+---
+id: xml-variant-ingestion
+title: XML Variant Ingestion
+sidebar_label: XML Variant Ingestion
+platform_key: DOCS_DNA_PIPELINE
+---
+
+The ARGO Data Platform accepts variant calling data in XML format (based on hg19 genome reference). The XML file will be converted to VCF file followed by lift over to GRCh38 reference genome. For details, please see the latest version of the [ARGO xml_variant_ingestion workflow](https://github.com/icgc-argo-workflows/dna-seq-processing-wfs/releases).
+
+## Inputs
+* Submitted XML file(s)
+* Mapping file
+* [GRCh38](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) as human reference genome
+* Genome liftover [chain file](https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/)
+* [Genome reference](https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/) used to call variant in the XML file
+
+## Processing
+* Submitted variant calling (XML) are converted into VCFs based on variant types (copy number alteration, rearrangement and short variant).
+* [Picard:liftovervcf](https://gatk.broadinstitute.org/hc/en-us/articles/27007978536219-LiftoverVcf-Picard) is used to lift the variant calling to GRCh38 reference genome.
+
+## Outputs
+* [Raw SNV Calls](https://docs.icgc-argo.org/docs/data/variant-calls#raw-snv-calls) and [VCF Index](https://docs.icgc-argo.org/docs/data/variant-calls#vcf-index)
+* [Raw Indel Calls](https://docs.icgc-argo.org/docs/data/variant-calls#raw-indel-calls) and [VCF Index](https://docs.icgc-argo.org/docs/data/variant-calls#vcf-index)
+* [Raw SV Calls](https://docs.icgc-argo.org/docs/data/variant-calls#raw-sv-calls) and [VCF Index](https://docs.icgc-argo.org/docs/data/variant-calls#vcf-index)
+* [Raw CNV Calls](https://docs.icgc-argo.org/docs/data/variant-calls#raw-cnv-calls) and [VCF Index](https://docs.icgc-argo.org/docs/data/variant-calls#vcf-index)
+
+## Workflow Diagram
+
+https://docs.google.com/drawings/d/1EfyRtN1mtX-iPNDvbdqTQLfvZ8iNPneGJZr-wS6U-dM/edit

docs/data/variant-calls.md

@@ -14,7 +14,7 @@ Data files containing Single Nucleotide Variations (SNV) called from aligned rea
 
 | Filename Pattern | Description                     | Analysis Type   | Data Category               | Generating Workflow(s)                                                                                                  |
 | ---------------- | ------------------------------- | --------------- | --------------------------- | ----------------------------------------------------------------------------------------------------------------------- |
-| \*.snv.vcf.gz    | SNV results in VCF File format. | variant_calling | Simple Nucleotide Variation | <ul><li>Sanger WGS Variant Calling </li><li>Sanger WXS Variant Calling </li><li> GATK Mutect2 Variant Calling</li></ul> |
+| \*.snv.vcf.gz    | SNV results in VCF File format. | variant_calling | Simple Nucleotide Variation | <ul><li>Sanger WGS Variant Calling </li><li>Sanger WXS Variant Calling </li><li>GATK Mutect2 Variant Calling </li><li>XML Variant Ingestion </li></ul> |
 
 ## SNV Supplement
 
@@ -34,7 +34,7 @@ Data files containing Structural Variations (SV) called from aligned reads, whic
 
 | Filename Pattern | Description                    | Analysis Type   | Data Category        | Generating Workflow(s)     |
 | ---------------- | ------------------------------ | --------------- | -------------------- | -------------------------- |
-| \*.sv.vcf.gz     | SV results in VCF File format. | variant_calling | Structural Variation | Sanger WGS Variant Calling |
+| \*.sv.vcf.gz     | SV results in VCF File format. | variant_calling | Structural Variation | <ul><li>Sanger WGS Variant Calling  </li><li>XML Variant Ingestion </li></ul> |
 
 ## SV Supplement
 
@@ -54,7 +54,7 @@ Data files containing the Copy Number Varations (CNV) called from aligned reads,
 
 | Filename Pattern | Description                     | Analysis Type   | Data Category         | Generating Workflow(s)     |
 | ---------------- | ------------------------------- | --------------- | --------------------- | -------------------------- |
-| \*.cnv.vcf.gz    | CNV results in VCF file format. | variant_calling | Copy Number Variation | Sanger WGS Variant Calling |
+| \*.cnv.vcf.gz    | CNV results in VCF file format. | variant_calling | Copy Number Variation | <ul><li>Sanger WGS Variant Calling  </li><li>XML Variant Ingestion </li></ul> |
 
 ## CNV Supplement
 
@@ -70,6 +70,12 @@ Data files containing CNV results and temporary files generated by variant calle
 
 Data files containing the simple Insertions and Deletions (InDel) data called from aligned reads, which have not yet been annotated but do have some filtering flags added.
 
+#### File Types
+
+| Filename Pattern | Description                     | Analysis Type   | Data Category         | Generating Workflow(s)     |
+| ---------------- | ------------------------------- | --------------- | --------------------- | -------------------------- |
+| \*.indel.vcf.gz    | CNV results in VCF file format. | variant_calling | Simple Nucleotide Variation | XML Variant Ingestion |
+
 ## InDel Supplement
 
 Data files containing InDel results and temporary files generated by variant callers used in the ARGO Analysis pipeline.
@@ -114,4 +120,4 @@ Secondary files that are external index files for VCF format files. TBI files fo
 
 | Filename Pattern | Description                                               | Analysis Type                                                | Data Category                                                                                            | Generating Workflow(s)                                                                                                                                        |
 | ---------------- | --------------------------------------------------------- | ------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| \*.vcf.gz.tbi    | VCF Index file format. Requires a corresponding VCF file. | <ul><li>variant_calling</li><li>variant_processing</li></ul> | <ul><li>Simple Nucleotide Variation</li><li>Structural Variation</li><li>Copy Number Variation</li></ul> | <ul><li>Sanger WGS Variant Calling </li><li>Sanger WXS Variant Calling </li><li> GATK Mutect2 Variant Calling</li><li>Open Access Variant Filtering</li></ul> |
+| \*.vcf.gz.tbi    | VCF Index file format. Requires a corresponding VCF file. | <ul><li>variant_calling</li><li>variant_processing</li></ul> | <ul><li>Simple Nucleotide Variation</li><li>Structural Variation</li><li>Copy Number Variation</li></ul> | <ul><li>Sanger WGS Variant Calling </li><li>Sanger WXS Variant Calling </li><li> GATK Mutect2 Variant Calling</li><li>Open Access Variant Filtering</li><li>XML Variant Ingestion </li></ul> |

website/sidebars.js

@@ -92,6 +92,7 @@ module.exports = {
             'analysis-workflows/dna-sanger-wgs-vc',
             'analysis-workflows/dna-sanger-wxs-vc',
             'analysis-workflows/dna-gatk-mutect2-vc',
+            'analysis-workflows/xml-variant-ingestion',
             'analysis-workflows/dna-open-access-filtering',
           ],
         },