Merge pull request #137 from molgenis/feat/new_features

Feat/new features + VEP update

README.md

@@ -11,12 +11,34 @@ below.
 CAPICE can be used as online service at http://molgenis.org/capice
 
 ## Requirements
-* VEP v105
+The list below is a complete list. Depending on whether GRCh37 and/or GRCh38 is used and whether all
+mentioned features are used, some items in the list below can be skipped.
+
+* VEP v107
+  * Including VEP cache (which needs to be unarchived!):
+    * [homo_sapiens_refseq_vep_107_GRCh37](http://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_refseq_vep_107_GRCh37.tar.gz)
+    * [homo_sapiens_refseq_vep_107_GRCh38](http://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_refseq_vep_107_GRCh38.tar.gz)
   * Including plugin(s):
-  * [SpliceAI](https://m.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceai)
+    * [Grantham](https://github.com/molgenis/vip/blob/master/resources/vep/plugins/Grantham.pm)
+    * [SpliceAI](https://github.com/molgenis/vip/blob/master/resources/vep/plugins/SpliceAI.pm)
+  * Including additional data (GRCh37) [available here](https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/):
+    * `gnomad.total.r2.1.1.sites.stripped.vcf.gz`
+    * `gnomad.total.r2.1.1.sites.stripped.vcf.gz.csi`
+    * `hg19.100way.phyloP100way.bw`
+    * `spliceai_scores.masked.indel.hg19.vcf.gz`
+    * `spliceai_scores.masked.indel.hg19.vcf.gz.tbi`
+    * `spliceai_scores.masked.snv.hg19.vcf.gz`
+    * `spliceai_scores.masked.snv.hg19.vcf.gz.tbi` 
+  * Including additional data (GRCh38) [available here](https://download.molgeniscloud.org/downloads/vip/resources/GRCh38/):
+    * `gnomad.genomes.v3.1.2.sites.stripped.vcf.gz`
+    * `gnomad.genomes.v3.1.2.sites.stripped.vcf.gz.csi`
+    * `hg38.phyloP100way.bw`
+    * `spliceai_scores.masked.indel.hg38.vcf.gz`
+    * `spliceai_scores.masked.indel.hg38.vcf.gz.tbi`
+    * `spliceai_scores.masked.snv.hg38.vcf.gz`
+    * `spliceai_scores.masked.snv.hg38.vcf.gz.tbi` 
 * BCF tools v1.14-1
 * Python >=3.8
-* [Stripped gnomAD allele frequency counts](https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz) with [indexing file](https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz.csi) (for GRCh38: [data](https://download.molgeniscloud.org/downloads/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz) + [indexing file](https://download.molgeniscloud.org/downloads/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz.csi))
 
 ## Install
 The CAPICE software is also provided in this repository for running CAPICE in your own environment. The following
@@ -67,13 +89,20 @@ In order to score your variants through CAPICE, you have to annotate your varian
 command:
 
 ```commandline
-vep --input_file <path to your input file> --format vcf --output_file <path to your output file> --vcf --compress_output gzip --force_overwrite 
---sift s --polyphen s --numbers --symbol --shift_3prime 1 --allele_number --refseq --total_length  
---no_stats --offline --cache --dir_cache </path/to/cache/105> --species "homo_sapiens" --assembly <GRCh37 or GRCh38> --fork 4 
---dont_skip --allow_non_variant --use_given_ref --exclude_predicted --flag_pick_allele
---plugin SpliceAI,snv=<path/to/raw_scores_snv.vcf.gz>,indel=</path/to/raw_scores_indel.vcf.gz> --dir_plugins <path to your VEP plugin directory>
---custom </path/to/stripped/gnomad.vcf.gz>,gnomAD,vcf,exact,0,AF,HN
+vep --input_file <path to your input file> --format vcf --output_file <path to your output file> \
+--vcf --compress_output gzip --sift s --polyphen s --numbers --symbol \
+--shift_3prime 1 --allele_number --refseq --total_length --no_stats --offline --cache \
+--dir_cache </path/to/cache/107> --species "homo_sapiens" --assembly <GRCh37 or GRCh38> \
+--fork <n_threads> --dont_skip --allow_non_variant --use_given_ref --exclude_predicted \
+--flag_pick_allele --plugin Grantham \
+--plugin SpliceAI,snv=<path/to/spliceai_scores.masked.snv.vcf.gz>,indel=</path/to/spliceai_scores.masked.indel.vcf.gz> \
+--custom "<path/to/gnomad.total.sites.stripped.vcf.gz>,gnomAD,vcf,exact,0,AF,HN" \
+--custom "<path/to/phyloP100way.bw>,phyloP,bigwig,exact,0" \
+--dir_plugins <path to your VEP plugin directory>
 ```
+**IMPORTANT: Ensure the right files are used based on GRCH37 or GRCH38!!!**
+
+Note: Certain arguments might not be needed if training/predicting without using all possible features offered by CAPICE.
 
 Then you have to convert the VEP output to TSV using our own BCFTools script: 
 `./scripts/convert_vep_vcf_to_tsv_capice.sh -i </path/to/vep_output.vcf.gz> -o </path/to/capice_input.tsv.gz>`

resources/train_features.json

@@ -58,5 +58,7 @@
     "SpliceAI_pred_DS_DG": null,
     "SpliceAI_pred_DS_DL": null,
     "Type": null,
-    "Length": null
+    "Length": null,
+    "Grantham": null,
+    "phyloP": null
 }

src/molgenis/capice/__init__.py

@@ -1 +1 @@
-__version__ = '4.0.0-rc2'
+__version__ = '4.0.0-rc3'