vep v78 => v81

Author: bw2

deploy/mac_osx/README.md

@@ -53,10 +53,10 @@ NOTE: root access may be required for the brew install commands.
 0. Download and install VEP. It's used by seqr to annotate variants. Also, we install tabix as we need it to optimize the VEP cache.  
    `brew install tabix`  
    `cd ${SEQR_INSTALL_DIR}`  
-   `wget https://github.com/Ensembl/ensembl-tools/archive/release/78.zip`  
-   `unzip 78.zip`  
-   `mv ensembl-tools-release-78/scripts/variant_effect_predictor .`  
-   `rm -rf 78.zip ensembl-tools-release-78`  
+   `wget https://github.com/Ensembl/ensembl-tools/archive/release/81.zip`  
+   `unzip 81.zip`  
+   `mv ensembl-tools-release-81/scripts/variant_effect_predictor .`  
+   `rm -rf 81.zip ensembl-tools-release-81`  
    `cd variant_effect_predictor`  
    `perl INSTALL.pl --AUTO acf --CACHEDIR ../vep_cache_dir --SPECIES homo_sapiens --ASSEMBLY  GRCh37 --CONVERT`  
 
@@ -145,7 +145,7 @@ NOTE: root access may be required for the brew install commands.
 
 0. Before a VCF can be loaded into seqr, it must be annotated with VEP to add a specific set of annotations, including those provided by the [dbNSFP](http://www.ensembl.info/ecode/loftee/) and [LoFTEE](http://www.ensembl.info/ecode/loftee/) plugins. Once these plugins have been installed, please use the following command to annotate your VCF file (here called my_data.vcf.gz): 
 
-   ```perl ./vep/ensembl-tools-release-78/scripts/variant_effect_predictor/variant_effect_predictor.pl --everything --vcf --allele_number --no_stats --cache --offline --dir ./vep_cache/ --force_overwrite --cache_version 78 --fasta ./vep_cache/homo_sapiens/78_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --assembly GRCh37 --tabix --plugin LoF,human_ancestor_fa:./loftee_data/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15 --plugin dbNSFP,./reference_data/dbNSFP/dbNSFPv2.9.gz,Polyphen2_HVAR_pred,CADD_phred,SIFT_pred,FATHMM_pred,MutationTaster_pred,MetaSVM_pred -i my_data.vcf.gz -o my_data.vep.vcf.gz```
+   ```perl ./vep/ensembl-tools-release-81/scripts/variant_effect_predictor/variant_effect_predictor.pl --everything --vcf --allele_number --no_stats --cache --offline --dir ./vep_cache/ --force_overwrite --cache_version 81 --fasta ./vep_cache/homo_sapiens/81_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --assembly GRCh37 --tabix --plugin LoF,human_ancestor_fa:./loftee_data/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15 --plugin dbNSFP,./reference_data/dbNSFP/dbNSFPv2.9.gz,Polyphen2_HVAR_pred,CADD_phred,SIFT_pred,FATHMM_pred,MutationTaster_pred,MetaSVM_pred -i my_data.vcf.gz -o my_data.vep.vcf.gz```
 
 0. Once you have an annotated file, it can be loaded the same way as steps 6 to 8 in the 'Load example data' section.