TIS - Update docs: replace topmed-r2 panel with topmed-r3

statgen · Dec 5, 2023 · 05359d5 · 05359d5
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commit 05359d5
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Showing 3 changed files with 13 additions and 17 deletions.
diff --git a/docs/api.md b/docs/api.md
@@ -26,7 +26,7 @@ The following parameters can be set:
 | job-name      | (user specified)                                  |               |          |
 | files         | /path/to/file                                     |               | **x**    |
 | mode          | `qconly`<br> `phasing` <br> `imputation`          | `imputation`  | **x**    |
-| refpanel      | `apps@topmed-r2`                                  | -             | **x**    |
+| refpanel      | `apps@topmed-r3`                                  | -             | **x**    |
 | phasing       | `eagle`<br> `no_phasing`                          | `eagle`       |          |
 | build         | `hg19`<br> `hg38`                                 | `hg19`        |          |
 | r2Filter      | `0` <br> `0.001` <br> `0.1` <br> `0.2` <br> `0.3` | `0`           |          |
@@ -53,7 +53,7 @@ curl https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2/jobs/submit/imputat
   -F "job-name=Documentation example (1000G - chr1 and 2)" \
   -F "files=@/path-to/filename_chr1.vcf.gz" \
   -F "files=@/path-to/filename_chr2.vcf.gz" \
-  -F "refpanel=apps@topmed-r2" \
+  -F "refpanel=apps@topmed-r3" \
   -F "build=hg38" \
   -F "phasing=eagle" \
   -F "population=all" \
@@ -76,19 +76,17 @@ Response:
 #### Submit one or more vcf files
 
 ```python3
-import json
-
 import requests
 
 # imputation server url
 base = 'https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2'
-token = 'YOUR-API-TOKEN';
+token = 'YOUR-API-TOKEN'
 
 # add token to header (see documentation for Authentication)
 headers = {'X-Auth-Token' : token }
 data = {
   'job-name': 'Documentation example (1000G - chr1 and 2)',
-  'refpanel': 'apps@topmed-r2',
+  'refpanel': 'apps@topmed-r3',
   'population': 'all',
   'build': 'hg38',
   'phasing': 'eagle',
@@ -97,8 +95,8 @@ data = {
 }
 
 # submit new job. This demonstrates multiple files, one per chromosome. Edit to send one or more chromosomes, as needed.
-vcf1 = '/path/to/filename_chr1.vcf.gz';
-vcf2 = '/path/to/filename_chr2.vcf.gz';
+vcf1 = '/path/to/filename_chr1.vcf.gz'
+vcf2 = '/path/to/filename_chr2.vcf.gz'
 
 with open(vcf1, 'rb') as f1, open(vcf2, 'rb') as f2:
     files = [
@@ -148,7 +146,7 @@ Response:
   "data": [
     {
       "app": null,
-      "application": "Genotype Imputation (Minimac4) 1.7.3",
+      "application": "Genotype Imputation (Minimac4) 1.8.0",
       "canceld": false,
       "complete": true,
       "currentTime": 1687898833855,
@@ -175,13 +173,11 @@ Response:
 ### Example: Python
 
 ```python
-import json
-
 import requests
 
 # imputation server url
 url = 'https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2'
-token = 'YOUR-API-TOKEN';
+token = 'YOUR-API-TOKEN'
 
 # add token to header (see authentication)
 headers = {'X-Auth-Token' : token }
@@ -219,7 +215,7 @@ Response:
 ```json
 {
   "app": null,
-  "application": "Genotype Imputation (Minimac4) 1.7.3",
+  "application": "Genotype Imputation (Minimac4) 1.8.0",
   "applicationId": "imputationserver",
   "canceld": false,
   "complete": true,

diff --git a/docs/reference-panels.md b/docs/reference-panels.md
@@ -8,8 +8,8 @@ The TOPMed panel consists of 194,512 haplotypes
 
 | ||
 | | |
-| Number of Samples | 97,256 |
-| Sites (chr1-22) |  308,107,085 |
+| Number of Samples | 133,597 |
+| Sites (chr1-22) |  445,600,184 |
 | Chromosomes | 1-22, X|
 | Imputation Server: | [https://imputation.biodatacatalyst.nhlbi.nih.gov](https://imputation.biodatacatalyst.nhlbi.nih.gov) |
 | Website: | [https://www.nhlbiwgs.org/](https://www.nhlbiwgs.org/) |

diff --git a/files/minimac4.yaml b/files/minimac4.yaml
@@ -1,8 +1,8 @@
 id: imputationserver
 name: Genotype Imputation (Minimac4)
-description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
+description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="https://topmedimpute.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38/hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
 version: 1.8.0-beta4
-website: https://imputationserver.readthedocs.io
+website: https://topmedimpute.readthedocs.io/en/latest/
 category:
 
 installation: