Update SpliceAI description

SpliceAI.pm

@@ -37,6 +37,8 @@ limitations under the License.
  SpliceAI is a deep neural network, developed by Illumina, Inc 
  that predicts splice junctions from an arbitrary pre-mRNA transcript sequence.
  By default, this plugin appends all scores from SpliceAI files.
+ The plugin works with any file outputed by the SpliceAI tool - Ensembl provides scores
+ for all SNVs overlapping MANE transcripts. For more details see: 1. Download the input files
 
  Delta score of a variant, defined as the maximum of (DS_AG, DS_AL, DS_DG, DS_DL), 
  ranges from 0 to 1 and can be interpreted as the probability of the variant being 
@@ -89,23 +91,27 @@ limitations under the License.
 
  1. Download the input files:
 
-  - The Illumina-generated files with the annotations for all possible substitutions (snv), 1 base insertions 
-  and 1-4 base deletions (indel), within genes are available through basespace 
-  (https://basespace.illumina.com/s/otSPW8hnhaZR). 
+  - Ensembl-generated files (only available for GRCh38)
+  We calculated SpliceAI scores for all possible substitutions (SNV) within MANE Select transcripts.
+  The scores are available through the Ensembl FTP at https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_plugins/
+  Note: Ensembl does not provide INDEL annotations, please use the Illumina's files for INDEL scores.
+  To know more details on how the scores were calculated please read:
+  https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_plugins/README
+
+  - Illumina-generated files
+  Illumina calculated scores for all possible substitutions (SNV), 1 base insertions
+  and 1-4 base deletions (INDEL), within genes are available through basespace
+  (https://basespace.illumina.com/s/otSPW8hnhaZR).
     - To download via Illumina's basespace:
-      1. Log-in to your Illumina account or sign-up (for free) if you do not have one. 
-      2. Once you're in, a "Share Project" pop-up will appear - click "accept". 
+      1. Log-in to your Illumina account or sign-up (for free) if you do not have one.
+      2. Once you're in, a "Share Project" pop-up will appear - click "accept".
       3. A smaller pop-up in the bottom right will then read "Share Accepted". Click "Predicting splicing from primary sequence".
       4. You will get a list of files. Select "genome_scores_v1.3".
-      5. You will get an info/landing page. Under "Analysis: genome_scores_v1.3", select "FILES". 
-      6. Click the file icon next to "genome_scores_v1.3" and you will get a list of available files. 
-      7. Click filenames to download the relevant files - note that raw/masked, hg19/hg38 and snv/indel files are available. 
-
-  - The Ensembl-generated files with the annotations for all possible substitutions (snv), 1 base insertions, within genes are available through Ensembl 
- (https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_plugins/). Ensembl does not provide indel annotations, however, 
- Ensembl-generated files include annotations for Ensembl MANE select transcripts for v107 and v110 releases. 
+      5. You will get an info/landing page. Under "Analysis: genome_scores_v1.3", select "FILES".
+      6. Click the file icon next to "genome_scores_v1.3" and you will get a list of available files.
+      7. Click filenames to download the relevant files - note that raw/masked, hg19/hg38 and snv/indel files are available.
 
- 2. Tabix the files (if derived from Illumina). .tbi files are provided for Ensembl-derived VCFs. 
+ 2. For Illumina files: tabix the files (.tbi files are provided for Ensembl-derived VCFs).
 
   - GRCh37:
   tabix -p vcf spliceai_scores.raw.snv.hg19.vcf.gz
@@ -122,8 +128,8 @@ limitations under the License.
   ./vep -i variations.vcf --plugin SpliceAI,snv=/path/to/spliceai_scores.raw.snv.hg38.vcf.gz,indel=/path/to/spliceai_scores.raw.indel.hg38.vcf.gz,cutoff=0.5
   ./vep -i variations.vcf --plugin SpliceAI,snv=/path/to/spliceai_scores.raw.snv.hg38.vcf.gz,indel=/path/to/spliceai_scores.raw.indel.hg38.vcf.gz,split_output=1
 
-  - Or with Ensembl files: 
-  ./vep -i variations.vcf --plugin SpliceAI,snv=/path/to/spliceai_scores.masked.snv.ensembl_mane.grch38.110.vcf.gz,indel=/path/to/spliceai_scores.masked.indel.hg38.vcf.gz
+  - Or with Ensembl files (only for SNV):
+  ./vep -i variations.vcf --plugin SpliceAI,snv=/path/to/spliceai_scores.masked.snv.ensembl_mane_v1.4.grch38.vcf.gz,indel=/path/to/spliceai_scores.masked.indel.hg38.vcf.gz
 
 =cut
 

plugin_config.txt

@@ -1117,11 +1117,12 @@ my $VEP_PLUGIN_CONFIG = {
       "form" => [
         {
           "name" => "file_type",
-          "label" => "Select analysis mode",
+          "label" => "Select input files",
           "type" => "dropdown",
+          "helptip" => "Select the type of scores for annotation. SpliceAI's authors recommend using raw files for alternative splicing analysis and masked files for variant interpretation.",
           "values" => [
-            { "value" => "snv", "caption" => "Masked scores (Ensembl/GENCODE v24 canonical transcripts)" },
-            { "value" => "snv_ensembl", "caption" => "Raw scores (Ensembl/GENCODE v37 MANE transcripts, SNV only)" }
+            { "value" => "snv", "caption" => "Masked scores for SNVs and INDELs from Illumina's pre-calculated scores" },
+            { "value" => "snv_ensembl", "caption" => "Raw scores for SNVs overlapping MANE Select transcripts; INDELs from Illumina's pre-calculated scores" }
           ],
           "value" => "snv",
         },