scout-browser 4.98.0__tar.gz → 4.100.0__tar.gz

{scout_browser-4.98.0 → scout_browser-4.100.0}/.github/PULL_REQUEST_TEMPLATE.md

@@ -12,7 +12,7 @@ This PR marks a new Scout release. We apply semantic versioning. This is a major
 1. `sudo -iu hiseq.clinical`
 1. `ssh localhost`
 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps`
-1. Stop the service with current deployed branch: `systemctl --user stop scout.target`
+1. Stop the service with current deployed branch: `systemctl --user stop scout@<name_of_currently_deployed_branch>`
 1. Start the scout service with the branch to test: `systemctl --user start scout@<this_branch>`
 1. Make sure the branch is deployed: `systemctl --user status scout.target`
 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](https://pax.scilifelab.se), which will release the allocated resource (`scout-stage`) to be used for testing by other users.

{scout_browser-4.98.0 → scout_browser-4.100.0}/CHANGELOG.md

@@ -4,6 +4,77 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+
+## [4.100]
+### Added
+- Button with link to cancerhotspots.org on variant page for cancer cases (#5359)
+- Link to ClinGen ACMG CSPEC Criteria Specification Registry from ACMG classification page (#5364)
+- Documentation on how to export data from the scout database using the command line (#5373)
+- Filter cancer SNVs by ClinVar oncogenicity. OBS: since annotations are still sparse in ClinVar, relying solely on them could be too restrictive (#5367)
+- Include eventual gene-matching WTS outliers on variantS page (Overlap column) and variant page (Gene overlapping non-SNVs table) (#5371)
+- Minor Allele Frequency (HiFiCNV) IGV.js track for Nallo cases (#5401)
+- A page showing all cases submitted to the Matchmaker Exchange, accessible from the institute's sidebar (#5378)
+- Variants' loader progress bar (#5411)
+### Changed
+- Allow matching compounded subcategories from SV callers e.g. DUP:INV (#5360)
+- Adjust the link to the chanjo2 gene coverage report to reflect the type of analyses used for the samples (#5368)
+- Gene panels open in new tabs from case panels and display case name on the top of the page (#5369)
+- When uploading research variants, use rank threshold defined in case settings, if available, otherwise use the default threshold of 8 (#5370)
+- Display genome build version on case general report (#5381)
+- On pull request template, fixed instructions on how to deploy a branch to the development server (#5382)
+- On case general report, when a variant is classified (ACMG or CCV), tagged, commented and also dismissed, will only be displayed among the dismissed variants (#5377)
+- If case is re-runned/re-uploaded with the `--keep-actions` tag, remember also previously assigned diseases, HPO terms, phenotype groups and HPO panels (#5365)
+- Case load config alias and updated track label for TIDDIT coverage tracks to accommodate HiFiCNV dito (#5401)
+- On variants page, compounds popup table, truncate the display name of compound variants with display name that exceeds 20 characters (#5404)
+- Update dataTables js (#5407)
+- Load variants command prints more clearly which categories of variants are being loaded (#5409)
+- Tooltips instead of popovers (no click needed) for matching indicators on variantS page (#5419)
+- Call chanjo2 coverage completeness indicator via API after window loading completes (#5366)
+- On ClinVar multistep submission form, silence warnings coming from missing HGVS version using Entrez Eutils (#5424)
+### Fixed
+- Style of Alamut button on variant page (#5358)
+- Scope of overlapping functions (#5385)
+- Tests involving the variants controllers, which failed when not run in a specific order (#5391)
+- Option to return to the previous step in each of the steps of the ClinVar submission form (#5393)
+- chanjo2 MT report for cases in build 38 (#5397)
+- Fixed some variantS view tests accessing database out of app context (#5415)
+- Display of matching manual rank on the SV variant page (#5419)
+- Broken `scout setup database` command (#5422)
+- Collecting submission data for cases which have been removed (#5421)
+- Speed up query for gene overlapping variants (#5413)
+- Removing submission data for cases which have been removed (#5430)
+
+## [4.99]
+### Added
+- De novo assembly alignment file load and display (#5284)
+- Paraphase bam-let alignment file load and display (#5284)
+- Parsing and showing ClinVar somatic oncogenicity anontations, when available (#5304)
+- Gene overlapping variants (superset of compounds) for SVs (#5332)
+- Gene overlapping variants for MEIs (#5332)
+- Gene overlapping variants for cancer (and cancer_sv) (#5332)
+- Tests for the Google login functionality (#5335)
+- Support for login using Keycloak (#5337)
+- Documentation on Keycloak login system integration (#5342)
+- Integrity check for genes/transcripts/exons files downloaded from Ensembl (#5353)
+- Options for custom ID/display name for PanelApp Green updates (#5355)
+### Changed
+- Allow ACMG criteria strength modification to Very strong/Stand-alone (#5297)
+- Mocked the Ensembl liftover service in igv tracks tests (#5319)
+- Refactored the login function into smaller functions, handling respectively: user consent, LDAP login, Google login, database login and user validation (#5331)
+- Allow loading of mixed analysis type cases where some individuals are fully WTS and do not appear in DNA VCFs (#5327)
+- Documentation available in dark mode, and expanded installation instructions (#5343)
+### Fixed
+- Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity) (#5300)
+- Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled (#5311)
+- Institute settings reset (#5309)
+- Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor (#5318)
+- Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38 (#5302)
+- Sashimi view page displaying an error message when Ensembl REST API (LiftOver) is not available (#5322)
+- Refactored the liftover functionality to avoid using the old Ensembl REST API (#5326)
+- Downloading of Ensembl resources by fixing the URL to the schug server, pointing to the production instance instead of the staging one (#5348)
+- Missing MT genes from the IGV track (#5339)
+- Paraphase and de novo assembly tracks could mismatch alignment sample labels - refactor to case specific tracks (#5357)
+
 ## [4.98]
 ### Added
 - Documentation on how to delete variants for one or more cases

{scout_browser-4.98.0 → scout_browser-4.100.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.98.0
+Version: 4.100.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
@@ -124,29 +124,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## Installation
 
-<!-- You can install the latest release of Scout using `pip`:
-
-```bash
-pip install scout-browser
-
-# ... to include optional coverage tools you would use:
-pip install scout-browser[coverage]
-```
-
-If you would like to install Scout for local development: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+pip install --editable .
+```
 
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).
 

{scout_browser-4.98.0 → scout_browser-4.100.0}/README.md

@@ -50,29 +50,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## Installation
 
-<!-- You can install the latest release of Scout using `pip`:
-
-```bash
-pip install scout-browser
-
-# ... to include optional coverage tools you would use:
-pip install scout-browser[coverage]
-```
-
-If you would like to install Scout for local development: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+pip install --editable .
+```
 
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).
 

scout_browser-4.100.0/docs/admin-guide/export.md

@@ -0,0 +1,221 @@
+# Exporting Data from Scout
+
+There are many scenarios where users may want to export information from Scout.
+This document outlines the available export options and how to use them via the command line.
+
+## Main `export` command:
+
+```
+scout export
+```
+
+## Available Export Commands
+
+Scout provides the following subcommands for data export:
+
+```
+Options:
+  --help  Show this message and exit.
+
+Commands:
+  cases        Export case data
+  database     Export the Scout MongoDB database
+  exons        Export exon regions
+  genes        Export genes
+  hpo_genes    Export HPO-associated genes
+  managed      Export managed variants
+  mt_report    Export a mitochondrial variants report
+  panel        Export gene panels
+  transcripts  Export transcripts
+  variants     Export variants
+  verified     Export verified variants
+```
+
+Each command is described in detail below.
+
+---
+
+## Exporting Cases (`cases`)
+
+Export case information based on institute, status, or various filters. When exporting cases, it is possible to restrict the list of he exported data by adding optional parameters:
+
+```
+Options:
+  --case-id TEXT                  Case ID to search for
+  -i, --institute TEXT            Institute ID
+  -r, --reruns                    Include rerun-requested cases
+  -f, --finished                  Include archived or solved cases
+  --causatives                    Include cases with causative variants
+  --research-requested            Include cases with research requested
+  --rerun-monitor                 Include cases with continuous rerun monitoring
+  --is-research                   Include cases in research mode
+  -s, --status [prioritized|inactive|active|solved|archived|ignored]
+                                  Filter by case status
+  --within-days INTEGER           Filter by event date (days ago)
+  --json                          Output result in JSON format
+```
+
+The command's output is a list of case documents in the same format as they are saved into the database (dictionaries). By specifying the `--json`, documents are printed in json format.
+
+---
+
+## Exporting the Database (`database`)
+
+Dump the entire Scout MongoDB database (or subsets).
+
+```
+Options:
+  -o, --out PATH       Output directory for the dump [default: ./dump]
+  --uri TEXT           MongoDB connection URI
+  --all-collections    Include variant collections
+  --help               Show this message and exit
+```
+
+---
+
+## Exporting Exons (`exons`)
+
+Export all exons or limit to a specific gene. Default format is a .bed file, but they can be exported as a json file by using the `--json` option.
+
+```
+Options:
+  -b, --build [37|38]             Genome build version
+  -hgnc, --hgnc-id INTEGER        Filter by HGNC ID
+  --json                          Output in JSON format
+```
+
+**Output Format:**
+A tab-delimited list with the following header:
+
+```
+#Chrom	Start	End	ExonId	Transcripts	HgncIDs	HgncSymbols
+```
+
+---
+
+## Exporting Genes (`genes`)
+
+Export all genes from the database. Default format is a .bed file, but they can be exported as a json file by using the `--json` option.
+
+```
+Options:
+  -b, --build [37|38|GRCh38]      Genome build version [default: 37]
+  --json                          Output in JSON format
+```
+
+**Output Format:**
+A tab-delimited list with the following header:
+
+```
+#Chromosome	Start	End	Hgnc_id	Hgnc_symbol
+```
+
+---
+
+## Exporting HPO-Associated Genes (`hpo_genes`)
+
+Export HGNC IDs for all genes associated with a given HPO term.
+
+**Example Usage:**
+
+```
+scout export hpo_genes HP:0000371
+```
+
+Result:
+
+```
+#Gene_id	Count
+9986	1
+9987	1
+9988	1
+6193	1
+7067	1
+```
+
+---
+
+## Exporting Managed Variants (`managed`)
+
+Export managed variants in VCF format.
+
+**Example Output (VCF):**
+
+```
+##fileformat=VCFv4.2
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Type of variant">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	1295250	.	C	T	.	.	END=1295250;TYPE=SNV
+..
+```
+
+---
+
+## Exporting Mitochondrial Reports (`mt_report`)
+
+Export a mitochondrial report for a given case.
+
+```
+Options:
+  --case_id TEXT    Required case ID
+  --outpath TEXT    Path to the output file
+  --test            Run in test mode
+```
+
+---
+
+## Exporting Gene Panels (`panel`)
+
+Export gene panels with clinical annotation in BED format.
+
+```
+Options:
+  -b, --build [37|38|GRCh38]      Genome build version [default: 37]
+  --version FLOAT                 Specify panel version
+  --bed                           Export in BED-like format
+```
+
+**Output Header (default format):**
+
+```
+#hgnc_id	symbol	disease_associated_transcripts	reduced_penetrance	mosaicism	database_entry_version	inheritance_models	custom_inheritance_models	comment
+```
+
+---
+
+## Exporting Transcripts (`transcripts`)
+
+Export a list of transcripts in BED format. Use the following command: `scout export transcripts`
+
+```
+Options:
+  -b, --build [37|38|GRCh38]      Genome build version [default: 37]
+```
+---
+
+## Exporting Causative Variants (`variants`)
+
+Export causative variants for a case or an institute. Output is VCF by default, or JSON if specified.
+
+```
+Options:
+  -c, --collaborator TEXT         Collaborator ID [default: cust000]
+  -d, --document-id TEXT          Search for a specific variant
+  --case-id TEXT                  Case ID to search for
+  --json                          Output in JSON format
+```
+
+---
+
+## Exporting Verified Variants (`verified`)
+
+Similar to the `variants` export, but limited to verified variants. Output is VCF by default, or JSON if specified.
+
+```
+Options:
+  -c, --collaborator TEXT         Collaborator ID [default: cust000]
+  -d, --document-id TEXT          Search for a specific variant
+  --case-id TEXT                  Case ID to search for
+  --json                          Output in JSON format
+```

{scout_browser-4.98.0 → scout_browser-4.100.0}/docs/admin-guide/load-config.md

@@ -22,6 +22,7 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **coverage_qc_report** _String_ Path to HTML file with coverage and QC report.
 - **default_gene_panels** _List of strings_ List of default gene panels. Variants from the genes in the gene panels specified will be shown when opening the case in scout.
 - **delivery_report** _String_: Path to HTML delivery report.
+- **exe_ver**: Pipeline detailed software versions (YAML)
 - **family(*)**  _String_ Unique ID of the case.
 - **family_name**  _String_ Optional name of the case.
 - **gene_fusion_report** _String_ Path to a static gene fusion report produced by [Arriba][arriba] containing only clinical fusions (a subset of all detected fusions).
@@ -32,9 +33,9 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **madeline** _String_ Path to a madeline pedigree file in XML format.
 - **multiqc** _String_ Path to a [multiqc][multiqc] report with arbitrary information.
 - **multiqc_rna** _String_ Path to a [nf-core/rnafusion multiqc][rna-multiqc] report with arbitrary information.
-- **omics_files** _List_
-  - **fraser**: _String_ Path to TSV file to parse WTS [DROP][drop] FRASER splice outlier omics variants as produded by e.g. [Tomte][tomte]
-  - **outrider**: _String_ Path to TSV file to parse WTS [DROP][drop] OUTRIDER expression outlier omics variants as produded by e.g. [Tomte][tomte]
+- **omics_files** _List_ List of multiomics results files for the case:
+    - **fraser** _String_ Path to TSV file to parse WTS [DROP][drop] FRASER splice outlier omics variants as produded by e.g. [Tomte][tomte]
+    - **outrider** _String_ Path to TSV file to parse WTS [DROP][drop] OUTRIDER expression outlier omics variants as produded by e.g. [Tomte][tomte]
 - **owner(*)**  _String_ Institute who owns current case. Must refer to existing institute.
 - **peddy_check** _String_ Path to a [peddy][peddy] ped check file.
 - **peddy_ped** _String_ Path to a [peddy][peddy] ped file with an analysis of the pedigree based on variant information.
@@ -42,6 +43,7 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **phenotype_terms** _List of strings_ List of phenotype terms.
 - **rank model version** _String_ Which rank model that was used when scoring the variants.
 - **rank_score_threshold** _Float_ Only include variants with a rank score above this threshold.
+- **reference_info**: Pipeline detailed reference file versions (YAML)
 - **RNAfusion_inspector** _String_ Path to HTML [nf-core/rnafusion inspector][rnafusion-inspector] report containing only clinical fusions (a subset of all detected fusions).
 - **RNAfusion_inspector_research** _String_ Path to HTML [nf-core/rnafusion inspector][rnafusion-inspector] report containing all detected fusions.
 - **RNAfusion_report** _String_ Path to HTML [nf-core/rnafusion report][rnafusion-report] containing only clinical fusions (a subset of all detected fusions).
@@ -51,6 +53,7 @@ Below are available configuration parameters for a Scout case. Names marked with
 - **samples** _List_ List of samples included in the case:
     - **alignment_path** _String_ Path to BAM/CRAM file to view alignments.
     - **analysis_type** _String_ Specifies the analysis type for the sample. Options: {wgs, wes, panel, unknown, external}.
+    - **assembly_alignment_path** _String_ Path to BAM/CRAM file to view de novo assembly alignments.
     - **bam_file** _String_ Path to BAM/CRAM file to view alignments **WARNING:** Soon to be deprecated, use *alignment_path*.
     - **bam_path** _String_ Path to BAM/CRAM file to view alignments **WARNING:** Soon to be deprecated, use *alignment_path*.
     - **capture_kit** _String_ Exome specifies the capture kit.
@@ -66,10 +69,12 @@ Below are available configuration parameters for a Scout case. Names marked with
     - **hrd** _Int_ Homologous recombination deficiency.
     - **is_sma** _Bool/None_ if SMA status determined - None if not done.
     - **is_sma_carrier**  _Bool/None_  # True / False if SMA carriership determined - None if not done.
+    - **minor_allele_frequency_wig** _String_ Path to minor allele frequency bigwig [Reference][hificnv].
     - **mitodel** _String_ Path to mitodel file.
     - **mother** _String/Int_ Sample ID for mother or 0.
     - **msi** _Int_ Microsatellite instability [0-60].
     - **mt_bam** _String_ Path to the reduced mitochondrial BAM/CRAM alignment file.
+    - **paraphase_alignment_path** _String_ Path to BAM/CRAM file to view Paraphase alignments [Reference][paraphase].
     - **phenotype(*)** _String_ Specifies the affection status {affected, unaffected, unknown}.
     - **reviewer** _List_ [Reference][srs]
       - **alignment** _String_ Path to BAM/CRAM file to view STR alignments
@@ -84,13 +89,13 @@ Below are available configuration parameters for a Scout case. Names marked with
     - **rhocall_wig** _String_ Path to WIG file to view alignments [Reference][rhocall].
     - **samlple_id(*)** _String_ Identifyer for a sample.
     - **sample_name**: _String_ Name of sample.
-    - **sex (*)**: _String_ One of: {male, female, unknown}. Sex of the sample in human readable format.
+    - **sex (*)** _String_ One of: {male, female, unknown}. Sex of the sample in human readable format.
     - **smn1_cn** _Int_ Copynumber.
     - **smn2_cn** _Int_ Copynumber.
     - **smn2delta78_cn** _Int_ Copynumber.
     - **splice_junctions_bed** _String_ Path to indexed junctions .bed.gz file
     - **subject_id** _String_ Individual identifier - multiple samples could belong to the same individual
-    - **tiddit_coverage_wig** _String_ Path to WIG file to view alignments [Reference][tiddit].
+    - **tiddit_coverage_wig** or **coverage_wig** _String_ Path to WIG file to view alignment coverage overview from e.g. [Reference][tiddit] or [Reference][hificnv].
     - **tissue_type** _String_ Sample tissue origin i.e. blood, muscle.
     - **tmb** _Int_ Tumor mutational burden [0, 1000] (tumor case only).
     - **tumor_purity** _Float_ Purity of tumor sample [0.1, 1.0] (tumor case only).
@@ -144,7 +149,9 @@ vcf_snv: scout/demo/643594.clinical.vcf.gz
 [arriba]: https://arriba.readthedocs.io/en/latest/
 [d4_file]: https://github.com/38/d4-format
 [drop]: https://github.com/gagneurlab/drop
+[hificnv]: https://github.com/PacificBiosciences/HiFiCNV
 [multiqc]: https://github.com/ewels/multiqc
+[paraphase]: https://github.com/PacificBiosciences/paraphase
 [peddy]: https://github.com/brentp/peddy
 [rna-multiqc]: https://nf-co.re/rnafusion/output#multiqc
 [rnafusion-inspector]: https://nf-co.re/rnafusion/output#fusioninspector
@@ -156,3 +163,5 @@ vcf_snv: scout/demo/643594.clinical.vcf.gz
 [tomte]: https://github.com/genomic-medicine-sweden/tomte
 [upd]: https://github.com/bjhall/upd
 [yaml]: https://yaml.org
+
+

{scout_browser-4.98.0 → scout_browser-4.100.0}/docs/admin-guide/login-system.md

@@ -1,6 +1,7 @@
 # Setting up a user login system
 
-Scout currently supports 3 types of login systems:
+Scout currently supports 4 types of login systems:
+  - [keycloak authentication via OpenID Connect](#keycloak-openid-connect-login-system)
   - [Google authentication via OpenID Connect](#google-openid-connect-login-system)
   - [LDAP authentication](#login-using-lightweight-directory-access-protocol)
   - [Simple authentication using userid](#simple-login-with-userid)
@@ -8,6 +9,30 @@ Scout currently supports 3 types of login systems:
 **Login systems are mutually exclusive so when you choose a system, it will become be the only way all users will have access to the Scout app.**
 
 
+## Keycloak OpenID Connect Login System
+
+If your organization uses Keycloak as a login provider, Scout can be configured to authenticate users (who are already registered in the Scout database) using Keycloak in a few simple steps.
+
+A small tutorial with basic settings (intended for testing only, not for production) is available [on this page](https://github.com/northwestwitch/keycloak_flask_auth?tab=readme-ov-file#keycloak_flask_auth).
+
+Assuming a Keycloak realm containing users is available, you can edit the Scout configuration file to enable this authentication method:
+
+```python
+KEYCLOAK = dict(
+    client_id="<name_of_client>",
+    client_secret="secret", # available on Keycloak's admin console, under client credentials
+    discovery_url="http://<url_to_keycloak_instance>/realms/<name_of_realm>/.well-known/openid-configuration",
+    logout_url="http://<url_to_keycloak_instance>/realms/<name_of_realm>/protocol/openid-connect/logout",
+)
+```
+
+**Please note**: For this setup to work, the Keycloak client must include the following parameter:
+
+`Valid redirect URIs: "http://<scout-uri>/authorized"`
+
+
+Users attempting to log in to Scout will be redirected to the Keycloak instance for authentication.
+
 ## Google OpenID Connect login system
 
 Scout supports Google account login via OpenID Connect. Before setting up the Google authentication system in Scout it is necessary to register the Scout application in the Google API console and obtain OAuth 2.0 credentials. A detailed guide on how to do this is available [at this link](https://developers.google.com/identity/protocols/oauth2/openid-connect).

{scout_browser-4.98.0 → scout_browser-4.100.0}/docs/admin-guide/updating-individuals.md

@@ -22,14 +22,17 @@ Options:
   --help              Show this message and exit.
 ```
 And the tracks that can be updated are the following:
+- assembly_alignment_path
 - bam_file
 - d4_file
 - rna_alignment_path
 - mt_bam
 - vcf2cytosure
+- paraphase_alignment_path
 - rhocall_bed
 - rhocall_wig
 - tiddit_coverage_wig
+- minor_allele_frequency_wig
 - upd_regions_bed
 - upd_sites_bed
 - rna_coverage_bigwig
@@ -54,6 +57,7 @@ The following files are used by the [igv.js](https://github.com/igvteam/igv.js/w
 | --------------------|:------------------------------------------------------------|
 | bam_file            | path to a bam/cram alignment file                           |
 | mt_bam              | path to a downsampled mitochondrial bam/cram alignment file |
+| minor_allele_frequency_wig | path to hificnv maf wig file                         |
 | rhocall_bed         | path to rhocall output bed file                             |
 | rhocall_wig         | path to rhocall output wig file                             |
 | tiddit_coverage_wig | path to tiddit wig coverage file                            |
@@ -63,7 +67,8 @@ The following files are used by the [igv.js](https://github.com/igvteam/igv.js/w
 `rhocall_bed` and `rhocall_wig` files are both obtained from [rhocall](https://github.com/dnil/rhocall),
 a software that calls and annotates autozygosity from VCF files.
 
-`tiddit_coverage_wig` files are obtained from [tiddit](https://github.com/SciLifeLab/TIDDIT), a software which in turn is used to call structural variants.
+`tiddit_coverage_wig` files are obtained from [tiddit](https://github.com/SciLifeLab/TIDDIT) or [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV), software which in turn is used to call structural variants.
+Similarly, `minor_allele_frequency_wig` files are obtained from [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV), a software which is also used to call structural variants.
 
 `upd_regions_bed` and `upd_sites_bed` files are created from VCF files using the [upd tool](https://github.com/bjhall/upd).
 

scout_browser-4.100.0/docs/faq.md

@@ -0,0 +1,25 @@
+# FAQ
+
+## My email is white listed but I can't log into Scout
+
+You can be logged into multiple Google accounts at the same time. If you are only logged into
+one account, it will automatically be used when you click "Login with Google".
+
+Visit [Google][google] and click your avatar in the top right corner and "Add account" and log with your Scout connected account. Next time you access Scout you will be presented with an option of which Google account to use.
+
+
+## What should my VCF format look like in detail?
+
+Scout will work to some degree with many a generic (ideally VEP annotated) VCF as input, but, if you have a choice, for best results out of the box, use an already well integrated pipeline.
+The most well tested pipelines for Scout viewing currently are [MIP](https://github.com/Clinical-Genomics/MIP) (RD SR) or [Nextflow-wgs](https://github.com/Clinical-Genomics-Lund/nextflow_wgs) (RD SR),
+[Balsamic](https://github.com/Clinical-Genomics/BALSAMIC) (somatic), [nf-core/RNAfusion](https://github.com/nf-core/rnafusion) (RNA fusion) and [tomte](https://github.com/genomic-medicine-sweden/tomte) (RNA expression)
+We fully support [nf-core/raredisease](https://github.com/nf-core/raredisease) and [nf-core/Nallo](https://github.com/genomic-medicine-sweden/nallo) (RD LRS). We also
+have compatibility with at least earlier versions of other pipelines e.g. [sarek](https://github.com/nf-core/sarek) (somatic) and [poorpipe](https://github.com/J35P312/poorpipe) (RD LRS).
+
+To use the full features of Scout, try to load pre-ranked variants (see [genmod](https://github.com/Clinical-Genomics/genmod)).
+An important take home for variant triage, especially of SVs, is that you need to get good local database frequency annotation going. We use [SVDB](https://github.com/J35P312/SVDB) and/or [loqusdb](https://github.com/Clinical-Genomics/loqusdb).
+
+Say hi to the developers in a GitHub issue or discussion, describe your pipeline and situation and we may be able to direct you.
+
+
+[google]: https://www.google.com