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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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Mismatch between cache and assembly for T2T #1628

Closed Heather1999 closed 4 months ago

Heather1999 commented 8 months ago

Describe the issue

I used the t2t cache file provided in "https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_08/indexed_vep_cache/"; However, there seems to be a mismatch between cache and assembly.

System

ensembl : 111.a6cc543 ensembl-funcgen : 111.5327cdd ensembl-io : 111.dbba8d6 ensembl-variation : 111.d616b1e ensembl-vep : 111.0

Full VEP command line

./vep -i /home/sealight1999/ASC_T2T/rmzero/AS_02_filtered.vcf -o /home/sealight1999/ASC_T2T/rmzero/AS_02_veped_mutect.vcf --offline --cache_version 111 --force --assembly T2TCHM13v2.0 --dir_cache /home/sealight1999/references/CHM13/vep/ > vep_AS_02_Mutect2.log 2>&1

Full error message

WARNING: line 1 skipped (chr1 381371 . C T . haplotype;normal_artifact;...): Chromosome chr1 not found in annotation sources or synonyms; chromosome chr1 does not overlap any features WARNING: line 2 skipped (chr1 381377 . G A . haplotype;normal_artifact;...): Chromosome chr1 not found in annotation sources or synonyms; chromosome chr1 does not overlap any features WARNING: line 3 skipped (chr1 409792 . C T . orientation;weak_evidence ...): Chromosome chr1 not found in annotation sources or synonyms; chromosome chr1 does not overlap any features WARNING: line 4 skipped (chr1 475470 . C T . normal_artifact;orientatio...): Chromosome chr1 not found in annotation sources or synonyms; chromosome chr1 does not overlap any features WARNING: line 5 skipped... it went on to Chrom Y.

nakib103 commented 8 months ago

Hello @Heather1999,

Thanks for your query!

I cannot reproduce the same error message you are getting, is it the full error message?

But I can see several issues with the vep command you provided not related to those errors -

Can you try running the command with these updates.

Best regards, Nakib

Heather1999 commented 8 months ago

Hello @nakib103 Thank you so much for your swift response!! I made the changes you mentioned (thanks a lot for that), However the full error messages remained: ./vep -i /home/sealight1999/ASC_T2T/rmzero/AS_02_filtered.vcf -o /home/sealight1999/ASC_T2T/rmzero/AS_02_veped_mutect.vcf --offline --species homo_sapiens_gca009914755v4 --cache_version 106 --force --assembly T2T-CHM13v2.0 --dir_cache /home/sealight1999/references/CHM13/vep/

WARNING: Chromosome chr1 not found in annotation sources or synonyms on line 1 WARNING: Chromosome chr2 not found in annotation sources or synonyms on line 378 WARNING: Chromosome chr3 not found in annotation sources or synonyms on line 622 WARNING: Chromosome chr4 not found in annotation sources or synonyms on line 793 WARNING: Chromosome chr5 not found in annotation sources or synonyms on line 941 WARNING: Chromosome chr6 not found in annotation sources or synonyms on line 1088 WARNING: Chromosome chr7 not found in annotation sources or synonyms on line 1279 WARNING: Chromosome chr8 not found in annotation sources or synonyms on line 1514 WARNING: Chromosome chr9 not found in annotation sources or synonyms on line 1601 WARNING: Chromosome chr10 not found in annotation sources or synonyms on line 1739 WARNING: Chromosome chr11 not found in annotation sources or synonyms on line 1882 WARNING: Chromosome chr12 not found in annotation sources or synonyms on line 2095 WARNING: Chromosome chr13 not found in annotation sources or synonyms on line 2325 WARNING: Chromosome chr14 not found in annotation sources or synonyms on line 2385 WARNING: Chromosome chr15 not found in annotation sources or synonyms on line 2476 WARNING: Chromosome chr16 not found in annotation sources or synonyms on line 2598 WARNING: Chromosome chr17 not found in annotation sources or synonyms on line 2721 WARNING: Chromosome chr18 not found in annotation sources or synonyms on line 2888 WARNING: Chromosome chr19 not found in annotation sources or synonyms on line 2942 WARNING: Chromosome chr20 not found in annotation sources or synonyms on line 3331 WARNING: Chromosome chr21 not found in annotation sources or synonyms on line 3393 WARNING: Chromosome chr22 not found in annotation sources or synonyms on line 3436 WARNING: Chromosome chrX not found in annotation sources or synonyms on line 3524 WARNING: Chromosome chrY not found in annotation sources or synonyms on line 3662 Could the issue stem from the upstream processing? Thank you!

nakib103 commented 8 months ago

Hi @Heather1999, Can you share the input file you are using if possible, so that I can try reproducing the issue?

Thanks

Heather1999 commented 8 months ago

Sure ! I've sent out invitation to you, please check. Thank you.

nakib103 commented 8 months ago

Hello @Heather1999,

Can you kindly attach the input file in this ticket if possible? Or, you can send the files to this address helpdesk@ensembl.org and refer to vep-issue 1628? Our outreach team will forward the files to me.

Best regards, Nakib

Heather1999 commented 4 months ago

Hello @nakib103 , Since the last post, I've decided to try another route. But ran into another issue today: -------------------- EXCEPTION -------------------- MSG: ERROR: SIFT not available

STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::check_sift_polyphen /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:168 STACK Bio::EnsEMBL::VEP::AnnotationSource::Cache::Transcript::new /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm:121 STACK Bio::EnsEMBL::VEP::CacheDir::get_all_AnnotationSources /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:150 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:121 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::run /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199 STACK toplevel /home/sealight1999/miniconda3/envs/vep_t2t/ensembl-vep/vep:233 Date (localtime) = Wed Jun 19 21:45:53 2024 Ensembl API version = 106

While the SIFT is indeed inside the vep data file (info.txt), the followings ar its content: species homo_sapiens_gca009914755v4 assembly T2T-CHM13v2.0 sift
polyphen
source_genebuild 2022-06 source_assembly T2T-CHM13v2.0 variation_cols chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,clin_sig_allele,pubmed,var_synonyms var_type tabix

could you look into this please? Thank you!!

nakib103 commented 4 months ago

Hello @Heather1999,

You are seeing this error because we do not have SIFT scores for T2T assembly in the vep cache. The info.txt shows that there is no SIFT (otherewise it would have s/p/b value similar to --sift command) data in the cache.

We will soon publish a blog about how to use SIFT with T2T assembly in VEP along with required files. Keep an eye on this page for update. Until then please avoid using --sift for now.

Best regards, Nakib

Heather1999 commented 4 months ago

Hello @nakib103 , Thank you for your swift response!! I did not use --sift as my command is as following: perl /home/user/app/vcf2maf/vcf2maf.pl --input-vcf input.varscan.indel.Somatic.hc.vcf \ --output-maf output.varscan.indel.Somatic.hc.maf \ --tumor-id T --normal-id N --vcf-tumor-id TUMOR --vcf-normal-id NORMAL \ --ref-fasta "${T2T}" -vep-data /home/user/ref/CHM13/vep \ --species homo_sapiens_gca009914755v4 \ --vep-path /home/user/miniconda3/envs/vep_t2t/ensembl-vep \ --ncbi-build T2T-CHM13v2.0

Does that mean I can't work with T2T version of somatic variant vcf at the moment? Thank you!

nakib103 commented 4 months ago

Hello @Heather1999,

This is command for vcf2maf tool. This is an external tool and is not maintained by us. I believe the tool uses the --sift option when running VEP. If this is not required, can you get into contact with team that maintains vcf2maf about how you can avoid running --sift?

Heather1999 commented 4 months ago

Hello @nakib103 , Sure, I'll look into that right away. However I am currently trying to run vep independently; When I use custom annotation it kept running into errors, could you kindly offer any opinion on why this couldn't work? Thank you so much! ./vep --cache -i /home/user/t2t/varscan2/AS_14/AS_14.varscan.indel.Somatic.hc.vcf -o AS_14.varscan.indel.Somatic.hc.vep.vcf --species homo_sapiens_gca009914755v4 --offline --dir_cache /home/user/references/CHM13/vep --assembly T2T-CHM13v2.0 --custom /home/user/references/CHM13/chm13v2.0_GENCODEv35_CAT_Liftoff.vep.sorted.gtf, t2t, gtf, exact -------------------- EXCEPTION -------------------- MSG: ERROR: No format specified for custom annotation source /home/sealight1999/references/CHM13/chm13v2.0_GENCODEv35_CAT_Liftoff.vep.sorted.gtf

nakib103 commented 4 months ago

You have space after the , in the --custom argument. It should be something like this - 

--custom /home/user/references/CHM13/chm13v2.0_GENCODEv35_CAT_Liftoff.vep.sorted.gtf,t2t,gtf,exact
Heather1999 commented 4 months ago

Thank you so much for all your help!!!