docs: fix broken links

Apply also some minor cosmetics for consistency.

Disclaimers related links are left alone.

docs/FAQs.md

@@ -89,7 +89,7 @@ providing actionable prescribing recommendations from authorities like CPIC and
 
 ### What happens if I provide an outside diplotype or phenotype for a gene also found in the VCF file?
 
-Outside calls provided by the user will override the results from the VCF file. Details about the relative priority of outside calls can be found on the [Outside Call Format page](docs/using/Outside-Call-Format.md/#activity-score-genes).
+Outside calls provided by the user will override the results from the VCF file. Details about the relative priority of outside calls can be found on the [Outside Call Format page](/using/Outside-Call-Format#activity-score-genes).
 
 
 
@@ -115,7 +115,7 @@ For the gene _CFTR_, "_Reference_" in the PharmCAT report corresponds to "_ivaca
 
 
 ### How to render PharmCAT outputs into a tabular-formatted file
-PharmCAT is designed to take a single-sample VCF file and generate an individual PGx report in JSON or HTML formats. To support data analysis, we provide scripts and examples that render PharmCAT JSON outputs to tabular-formatted files. You can follow the instructions on this [PharmCAT multi-sample analysis page](https://pharmcat.org/technical-docs/multi-sample-analysis) for how to convert PharmCAT JSONs into TSV or CSV files.
+PharmCAT is designed to take a single-sample VCF file and generate an individual PGx report in JSON or HTML formats. To support data analysis, we provide scripts and examples that render PharmCAT JSON outputs to tabular-formatted files. You can follow the instructions on this [PharmCAT multi-sample analysis page](/using/Multi-Sample-Analysis) for how to convert PharmCAT JSONs into TSV or CSV files.
 
 ### Create one's own PDF report based on the PharmCAT .JSON file
 

docs/Genes-and-Drugs.md

@@ -45,7 +45,7 @@ These genes will not get allele matches from PharmCAT<sup>*</sup>. However, you
 matching recommendation data.
 
 See [Outside Call Format](/using/Outside-Call-Format) for formatting details and
-[Calling-CYP2D6.md](/using/Calling-CYP2D6.md) or [Calling-HLA.md](/using/Calling-HLA.md) for how to obtain CYP2D6 or
+[Calling CYP2D6](/using/Calling-CYP2D6) or [Calling HLA](/using/Calling-HLA) for how to obtain CYP2D6 or
 HLA calls, respectively, using sequencing data.
 
 | Gene | CPIC | PharmGKB-DPWG |

docs/index.md

@@ -17,7 +17,7 @@ pharmcat_version: 2.9.0
 </span>
 
 
-An active area of genomic medicine implementation at many healthcare organizations and academic medical centers includes development of decision support and return of results around pharmacogenomics.  One of the challenges in implementing pharmacogenomics is the representation of the information in clinical dosing guidelines, including star-allele haplotypes, and extracting these variants and haplotypes from genetic datasets.  In a collaboration between the [Pharmacogenomics Knowledgebase (PharmGKB)](https://www.pharmgkb.org) and the former [PGRN Statistical Analysis Resource (P-STAR)](http://www.pgrn.org/p-star.html), with input from other groups, we are developing a software tool to extract guideline variants from a genetic dataset (represented as a vcf), interpret the variant alleles, and generate a report with genotype-based prescribing recommendations which can be used to inform treatment decisions.
+An active area of genomic medicine implementation at many healthcare organizations and academic medical centers includes development of decision support and return of results around pharmacogenomics.  One of the challenges in implementing pharmacogenomics is the representation of the information in clinical dosing guidelines, including star-allele haplotypes, and extracting these variants and haplotypes from genetic datasets.  In a collaboration between the [Pharmacogenomics Knowledgebase (PharmGKB)](https://www.pharmgkb.org) and the former [PGRN Statistical Analysis Resource (P-STAR)](https://ritchielab.org/pgrn-star/), with input from other groups, we are developing a software tool to extract guideline variants from a genetic dataset (represented as a vcf), interpret the variant alleles, and generate a report with genotype-based prescribing recommendations which can be used to inform treatment decisions.
 
 The [Clinical Pharmacogenetics Implementation Consortium (CPIC)](https://cpicpgx.org) has established guidelines surrounding gene-drug pairs that can and should lead to treatment modifications based on genetic variants.  These guidelines are used for the initial version of PharmCAT, and other sources of PGx information and guidelines will be included in the future.
 

docs/using/Calling-HLA.md

@@ -119,7 +119,7 @@ Although we did not simulate coverage, a recent study by [Thuesen et al. 2022](h
 
 ## Working with HLA in PharmCAT
 
-PharmCAT supports incorporating results from your favorite HLA programs for phenotype translations through “[outside calls](https://pharmcat.org/using/Outside-Call-Format/).”
+PharmCAT supports incorporating results from your favorite HLA programs for phenotype translations through “[outside calls](/using/Outside-Call-Format).”
 
 To incorporate the outside calls, you would run PharmCAT as you normally would, and add the -po flag which signals the program to look for an external call file. Please note that PharmCAT requires that your HLA call have only two fields for phenotype translations. Therefore, if your external calls have more than two fields, you should truncate your output to only two fields. For more information on HLA nomenclature and what the each field means in HLA, please visit the page for [Nomenclature for Factors of the HLA System page](https://hla.alleles.org/nomenclature/naming.html). For example:
 
@@ -139,9 +139,9 @@ HLA-B	*07:02/*35:01
 
 For more information:
 
--   see [Running PharmCAT](https://pharmcat.org/using/Running-PharmCAT#phenotyper) for details on the -po flag
+-   see [Running PharmCAT](/using/Running-PharmCAT#phenotyper) for details on the -po flag
 
--   see [Outside Call Format](https://pharmcat.org/using/Outside-Call-Format) for details on the outside call file
+-   see [Outside Call Format](/using/Outside-Call-Format) for details on the outside call file
 
 ### Formatting Optitype output for PharmCAT
 

docs/using/index.md

@@ -14,8 +14,8 @@ Running PharmCAT:
 * [Running the full PharmCAT Pipeline](Running-PharmCAT-Pipeline)
 * [Running PharmCAT in Docker](PharmCAT-in-Docker)
 * [Multi-Sample Analysis](Multi-Sample-Analysis)
-* [Calling-CYP2D6](Calling-CYP2D6)
-* [Calling-HLA](Calling-HLA)
+* [Calling CYP2D6](Calling-CYP2D6)
+* [Calling HLA](Calling-HLA)
 
 Input file specifications: