1.4.3 release

Author: sigven

README.md

@@ -15,6 +15,8 @@ The germline variant annotator (*gvanno*) is a software package intended for ana
 *gvanno* accepts query files encoded in the VCF format, and can analyze both SNVs and short InDels. The workflow relies heavily upon [Ensembl’s Variant Effect Predictor (VEP)](http://www.ensembl.org/info/docs/tools/vep/index.html), and [vcfanno](https://github.com/brentp/vcfanno). It produces an annotated VCF file and a file of tab-separated values (.tsv), the latter listing all annotations pr. variant record. Note that if your input VCF contains data (genotypes) from multiple samples (i.e. a multisample VCF), the output TSV file will contain one line/record __per sample variant__.
 
 ### News
+* August 25th 2021 - **1.4.3 release**
+	* Data updates: ClinVar, GWAS catalog, CancerMine, UniProt, Open Targets Platform
 * May 24th 2021 - **1.4.2 release**
   * Software update (VEP 104)
   * Data updates: ClinVar, GWAS catalog, CancerMine, Pfam, dbNSFP, UniProt
@@ -32,12 +34,12 @@ The germline variant annotator (*gvanno*) is a software package intended for ana
 * [gnomAD](http://gnomad.broadinstitute.org/) - Germline variant frequencies exome-wide (release 2.1, October 2018) - from VEP
 * [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) - Database of short genetic variants (build 154) - from VEP
 * [1000 Genomes Project - phase3](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) - Germline variant frequencies genome-wide (May 2013) - from VEP
-* [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - Database of variants related to human health/disease phenotypes (May 2021)
-* [CancerMine](http://bionlp.bcgsc.ca/cancermine/) - literature-mined database of drivers, oncogenes and tumor suppressors in cancer (version 35)
-* [Open Targets Platform](https://targetvalidation.org) - Target-disease and target-drug associations (2021_02, February 2021)
-* [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - Resource on protein sequence and functional information (2021_02, April 2021)
+* [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - Database of variants related to human health/disease phenotypes (August 2021)
+* [CancerMine](http://bionlp.bcgsc.ca/cancermine/) - literature-mined database of drivers, oncogenes and tumor suppressors in cancer (version 38, August 2021)
+* [Open Targets Platform](https://targetvalidation.org) - Target-disease and target-drug associations (2021_06, June 2021)
+* [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - Resource on protein sequence and functional information (2021_03, June 2021)
 * [Pfam](http://pfam.xfam.org) - Database of protein families and domains (v34.0, March 2021)
-* [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/home) - Catalog of published genome-wide association studies (May 19th 2021)
+* [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/home) - Catalog of published genome-wide association studies (August 16th 2021)
 
 
 ### Getting started
@@ -71,17 +73,17 @@ An installation of Python (version >=_3.6_) is required to run *gvanno*. Check t
 
 #### STEP 2: Download *gvanno* and data bundle
 
-1. [Download the latest version](https://github.com/sigven/gvanno/releases/tag/v1.4.2) (gvanno run script, v1.4.2)
+1. [Download the latest version](https://github.com/sigven/gvanno/releases/tag/v1.4.3) (gvanno run script, v1.4.3)
 2. Download (preferably using `wget`) and unpack the latest assembly-specific data bundle in the gvanno directory
-   * [grch37 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20210523.tgz) (approx 19Gb)
-   * [grch38 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch38.20210523.tgz) (approx 20Gb)
+   * [grch37 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20210825.tgz) (approx 19Gb)
+   * [grch38 data bundle](http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch38.20210825.tgz) (approx 20Gb)
    * Example commands:
-	* `wget http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20210523.tgz`
+	* `wget http://insilico.hpc.uio.no/pcgr/gvanno/gvanno.databundle.grch37.20210825.tgz`
 	* `gzip -dc gvanno.databundle.grch37.YYYYMMDD.tgz | tar xvf -`
 
-    A _data/_ folder within the _gvanno-1.4.2_ software folder should now have been produced
-3. Pull the [gvanno Docker image (1.4.2)](https://hub.docker.com/r/sigven/gvanno/) from DockerHub (approx 2.4Gb):
-   * `docker pull sigven/gvanno:1.4.2` (gvanno annotation engine)
+    A _data/_ folder within the _gvanno-1.4.3_ software folder should now have been produced
+3. Pull the [gvanno Docker image (1.4.3)](https://hub.docker.com/r/sigven/gvanno/) from DockerHub (approx 2.2Gb):
+   * `docker pull sigven/gvanno:1.4.3` (gvanno annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -110,7 +112,7 @@ Run the workflow with **gvanno.py**, which takes the following arguments and opt
 	--query_vcf QUERY_VCF
 				    VCF input file with germline query variants (SNVs/InDels).
 	--gvanno_dir GVANNO_DIR
-				    Directory that contains the gvanno data bundle, e.g. ~/gvanno-dev
+				    Directory that contains the gvanno data bundle, e.g. ~/gvanno-1.4.3
 	--output_dir OUTPUT_DIR
 				    Output directory
 	--genome_assembly {grch37,grch38}
@@ -146,10 +148,10 @@ Run the workflow with **gvanno.py**, which takes the following arguments and opt
 
 The _examples_ folder contains an example VCF file. Analysis of the example VCF can be performed by the following command:
 
-	python ~/gvanno-1.4.2/gvanno.py
-	--query_vcf ~/gvanno-1.4.2/examples/example.grch37.vcf.gz
-	--gvanno_dir ~/gvanno-1.4.2
-	--output_dir ~/gvanno-1.4.2
+	python ~/gvanno-1.4.3/gvanno.py
+	--query_vcf ~/gvanno-1.4.3/examples/example.grch37.vcf.gz
+	--gvanno_dir ~/gvanno-1.4.3
+	--output_dir ~/gvanno-1.4.3
 	--sample_id example
 	--genome_assembly grch37
 	--container docker

data-raw/RELEASE_NOTES

@@ -1,14 +1,14 @@
 ##GVANNO_SOFTWARE_VERSION = 1.4.3
-##GVANNO_DB_VERSION = 20210523
+##GVANNO_DB_VERSION = 20210825
 pfam = v34.0 (March 2021)
 ncER = v1.0 (March 2019)
-uniprot = release 2021_02
+uniprot = release 2021_03
 corum = release 3.0 (20180903)
 onekg = phase 3 (20130502)
 dbsnp = build 154/153
-dbnsfp = v4.2 (March 2021)
+dbnsfp = v4.2 (April 2021)
 gnomad = r2.1 (October 2018)
-gwas = May 2021 (20210519)
-clinvar = May 2021 (20210501)
-opentargets = 2021_02
+gwas = August 2021 (20210816)
+clinvar = August 2021 (20210731)
+opentargets = 2021_06
 gencode = 38/19

gvanno.py

@@ -11,8 +11,8 @@
 import platform
 from argparse import RawTextHelpFormatter
 
-GVANNO_VERSION = '1.4.2'
-DB_VERSION = 'GVANNO_DB_VERSION = 20210523'
+GVANNO_VERSION = '1.4.3'
+DB_VERSION = 'GVANNO_DB_VERSION = 20210825'
 VEP_VERSION = '104'
 GENCODE_VERSION = '38'
 VEP_ASSEMBLY = "GRCh38"

src/.DS_Store

@@ -165,7 +165,7 @@ ENV PERL5LIB $PERL5LIB_TMP
 WORKDIR /
 ADD loftee_1.0.3.tgz $OPT/src/ensembl-vep/modules
 ADD UTRannotator.tgz $OPT/src/ensembl-vep/modules
-RUN wget -q "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/103/NearestExonJB.pm" -O $OPT/src/ensembl-vep/modules/NearestExonJB.pm
+RUN wget -q "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/104/NearestExonJB.pm" -O $OPT/src/ensembl-vep/modules/NearestExonJB.pm
 
 
 # Final steps