REVEL plugin: pre-processing of the REVEL scores

[d-deen]

There is an update of the revel scores "February 5, 2020: All files now include GRCh38 positions (computed using liftOver) in addition to hg19/GRCh37 positions", and the instructions for the pre-processing of the file to make it work with REVEL plugin doesn't seem to take into account these changes. Can you please update the instructions/plugin?

[at7]

The documentation for processing the REVEL files based on the assembly version used is here. Please let me know if you have any more questions.

Best wishes, Anja

[longpanfr]

hello, I also have same problem. I used the method provided by you to process the REVEL files. I just checked the script of REVEL plugin and the data table of REVEL. The following table is the format of REVEL file. There is no "start" and "end" column which will be retrieved in the script "REVEL.pm". In fact, I am not sure about this since I am not familiar with perl script?

REVEL Data: chr hg19_pos grch38_pos ref alt aaref aaalt REVEL 1: 1 35142 35142 G A T M 0.027 2: 1 35142 35142 G C T R 0.035 3: 1 35142 35142 G T T K 0.043 4: 1 35143 35143 T A T S 0.018 5: 1 35143 35143 T C T A 0.034 6: 1 35143 35143 T G T P 0.039

The documentation for processing the REVEL files based on the assembly version used is here. Please let me know if you have any more questions.

Best wishes, Anja

[at7]

Hi, I can see now that the additional column _grch38pos is causing a problem in the plugin code. We will work on a fix and update you when this issue has been resolved.

Best wishes, Anja

[longpanfr]

thank you! long

[at7]

Hello, we have updated the plugin to work with the latest REVEL file which also includes the GRCh38 positions. The updated plugin is available with the latest release 104.

Best wishes, Anja

[longpanfr]

good news, thank you!

Anja Thormann @.***> 于2021年5月6日周四 上午11:53写道：

Hello, we have updated the plugin to work with the latest REVEL file which also includes the GRCh38 positions. The updated plugin is available with the latest release 104.

Best wishes, Anja

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[d-deen]

Hello, The updated plugin is still not working for me. I updated the plugin from the latest release and followed the pre-processing steps. This is an error I kept getting:

"Use of uninitialized value $assembly in hash element at //ensembl-vep/Plugins/REVEL.pm line 105. Use of uninitialized value in string eq at //ensembl-vep/Plugins/REVEL.pm line 105. "WARNING: Failed to instantiate plugin REVEL: ERROR: Assembly is but REVEL file does not contain in header."

[at7]

Hello, could you please share your full VEP command?

Thank you, Anja

[d-deen]

This is my full command:

${vep_path}/vep --cache --dir $dir \ --dir_cache $dir_cache \ --offline \ --fasta $fasta \ --species homo_sapiens \ --input_file ${Out}/${Job}_report/${Job}_filtered_cohort.vcf.gz \ --output_file ${Out}/${Job}_report/${Job}_filtered_cohort_annotated.vcf \ --format vcf \ --force_overwrite \ --vcf \ --no_check_variants_order \ --check_existing \ --freq_pop gnomAD \ --stats_file ${Out}/${Job}_report/${Job}_vep_stat.html \ --warning_file ${Out}/${Job}_logs/${Job}_vep_warning.txt \ --hgvs \ --variant_class \ --keep_csq \ --af_gnomad \ --polyphen p \ --sift p \ --symbol \ --total_length \ --max_af \ --plugin CADD,/nobackup/proj/rtmngs/Mt_Exome_pipeline/genomes/Plugins/CADD/whole_genome_SNVs.tsv.gz,/nobackup/proj/rtmngs/Mt_Exome_pipeline/genomes/Plugins/CADD/InDels.tsv.gz \ --plugin dbNSFP,/nobackup/proj/rtmngs/Mt_Exome_pipeline/DD/programs_DD/ensembl-vep/Plugins/dbNSFP4.1a_grch38.gz,MutationTaster_pred \ --plugin ExACpLI,/nobackup/proj/rtmngs/Mt_Exome_pipeline/DD/programs_DD/ensembl-vep/Plugins/ExACpLI_values.txt \ --plugin LoFtool \ --plugin DisGeNET,file=/nobackup/proj/rtmngs/Mt_Exome_pipeline/DD/programs_DD/ensembl-vep/Plugins/all_variant_disease_pmid_associations_final.tsv.gz,disease=1 \ --plugin Mastermind,/nobackup/proj/rtmngs/Mt_Exome_pipeline/DD/programs_DD/ensembl-vep/Plugins/mastermind_cited_variants_reference-2021.04.02-grch38.vcf.gz,0,0,1 \ --plugin REVEL,/nobackup/ndd73/revel/revel-old/new_tabbed_revel_grch38.tsv.gz --fields "Gene,Feature,SYMBOL,Existing_variation,VARIANT_CLASS,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,HGVSc,HGVSp,BIOTYPE,IMPACT,CLIN_SIG,PolyPhen,SIFT,CADD_PHRED,CADD_RAW,MutationTaster_pred,gnomAD_AF,MAX_AF,ExACpLI,LoFtool,DisGeNET_PMID,DisGeNET_SCORE,DisGeNET_disease,Mastermind_URL,REVEL" \ --pick \ --pick_order rank,canonical,tsl \ --buffer_size 20000 \ --fork 4

The rest of the annotation does work apart from REVEL.

[d-deen]

And this is the header of new_tabbed_revel_grch38.tsv

chr hg19_pos grch38_pos ref alt aaref aaalt REVEL

1 35142 35142 G A T M 0.027 1 35142 35142 G C T R 0.035 1 35142 35142 G T T K 0.043 1 35143 35143 T A T S 0.018 1 35143 35143 T C T A 0.034

[at7]

Thank you for sharing your VEP command. Could you please add --assembly GRCh38 to your VEP command and then rerun to see if this fixes the REVEL plugin?

Thank you, Anja

[d-deen]

Thanks Anja, now it is working!

[git-jemiller]

Hello, I'm getting an error related to unexpected numbers of columns when I try and use REVEL. VEP is working for me well otherwise with these files. I think this is because in early May the REVEL authors updated the annotation file (file name also changed FYI) to include transcriptID but I could be wrong. It seems like every time they update the file this thread gets bumped : (

New file after formatting

$ zcat cache/new_tabbed_revel_grch38.tsv.gz | head
#chr    hg19_pos    grch38_pos  ref alt aaref   aaalt   REVEL   Ensembl_transcriptid
1   35142   35142   G   A   T   M   0.027   ENST00000417324
1   35142   35142   G   C   T   R   0.035   ENST00000417324
1   35142   35142   G   T   T   K   0.043   ENST00000417324
1   35143   35143   T   A   T   S   0.018   ENST00000417324
1   35143   35143   T   C   T   A   0.034   ENST00000417324
1   35143   35143   T   G   T   P   0.039   ENST00000417324
1   35144   35144   A   C   C   W   0.012   ENST00000417324
1   35145   35145   C   A   C   F   0.023   ENST00000417324
1   35145   35145   C   G   C   S   0.029   ENST00000417324

#attempting to run VEP with REVEL
$VEP -i ukb23155_c17_b0_v1_mapt.input2 --species homo_sapiens --offline --force --cache --dir $CacheDIR --cache_version 104 -assembly GRCh38 -o ukb23155_c17_b0_v1_mapt.output2.revel --force_overwrite --plugin REVEL,/work/genomics/tools/ensembl-vep_104/Plugins/cache/new_tabbed_revel_grch38.tsv.gz --dir_plugins /work/genomics/tools/ensembl-vep_104/Plugins/
WARNING: Failed to instantiate plugin REVEL: ERROR: Column count must be 8 for REVEL files with GRCh38 positions or 7 for REVEL files with GRCh37 positions only.

$

Could the processing instructions or code be updated to account for this change? Thanks!

[olaaustine]

Hi, I can see how the additional column may be causing an issue. We will work on a fix to account for this change. Thank you, Ola.

[olaaustine]

Hi Jason, We have made a quick fix to allow you use the updated file version, Thanks for bringing this to our notice. Do let us know if you have any other questions. Thanks, Ola.

[git-jemiller]

Hi Ola, I just tested the updated code out and it's working as expected now. Thanks for fixing this issue in a timely manner!