susannasiebert
commented
3 months ago Did you use the --pass-only flag when running pVACseq the second time with your soft-filtered VCF? Otherwise pVACseq will still try to process all entries, irregardless of filter status.
Either way I would be concerned about the unusually high mismatch rate the ref-transcript-mismatch-reporter reported (Percentage of processable transcripts with mismatched annotations: 66.91%). That means of all variant types that pVACseq supports, 66.91% have a mismatched transcript which might indicate that there could be a mismatch in the references used at some point in your pipeline. I would carefully investigate your pipeline to ensure that the same ensembl version, reference build version, and reference fasta are being used throughout. If all those are consistent throughout variant calling and annotation, these mismatches should be rare to non-existent. This could potentially also explain the high number of frameshift_variant transcript does not contain a FrameshiftSequence warnings you are seeing. Once you confirm that all your reference data is indeed consistent throughout your pipeline, moving forward with the filtered VCF would indeed be the right approach.
dincerkilic
Installation Type
Standalone
pVACtools Version / Docker Image
4.2.1
Python Version
Python 3.11.6
Operating System
No response
Describe the bug
Hello, I use the comand below to annotate my VCF file. No problem occurs at this step.
../ensembl-vep/vep -i BSWC_NMO_P61.final.vcf -o out_vep/out_BSWC_NMO_P61.final.vcf --format vcf --vcf --symbol --terms SO --tsl --biotype --hgvs --offline --cache --dir_cache /home/ubuntu/.vep/ --plugin Frameshift --plugin Wildtype --dir_plugins /home/ubuntu/.vep/Plugins/ --species mus_musculus --fasta ../../İndirilenler/mm10.faHowever, I get the output below while running pvac run with the command below:pvacseq run out_vep/out_BSWC_NMO_P61.final.vcf BSWC_NMO_P61 H-2-Db,H-2-Dd,H-2-Dk,H-2-Dp,H-2-Kb,H-2-Kd,H-2-Kk,H-2-Kq,H-2-Ld,H-2-Lq,H2-IAb,H2-IAd,H2-IEd BigMHC_EL BigMHC_IM DeepImmuno NNalign NetMHC NetMHCIIpan NetMHCIIpanEL NetMHCcons NetMHCpan NetMHCpanEL SMM SMMPMBEC SMMalign out_pvac -t 6Then I run;
ref-transcript-mismatch-reporter out_vep_BSWC_NMO_P61/out_BSWC_NMO_P61.final.vcf --filter softAnd output below:
With the out_BSWC_NMO_P61.final.filtered.vcf file, I run pvac run again and I get error:
Do you have an idea how to fix the problem? Thank you in advance!
How to reproduce this bug
Input files
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Log output
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Output files
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