-
Notifications
You must be signed in to change notification settings - Fork 114
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Missing ZYG field from VEP output #724
Comments
Hi @IanCodes, The option Let me know if you have more questions. Best wishes, |
@dglemos Thank you very much for your reply Diana appears to be just what i need. |
I'm glad it worked! Best wishes, |
Apologies for the follow up, but I am observing that when I use '--individual_zyg all' I receive fewer lines of VEP output when using the same VCF file. Are there types of variant that are not processed using this flag? |
Can you show me an example please? |
Thank you for your fast response. I have with and without ZYG files, but they are big. What would be the best method of sharing them? |
You can send your files to [email protected] or if they are too big to send by email, you can send a sample of the files. |
I have extracted chr10 results for the VEP output with and without ZYG . Thank you. |
Thank you! |
Sorry for the delay here is the chr10 part of the VCF file (and headers). There were a number of plugins with huge files. No sure how well you'll be able to repeat my analysis. Let me know if you need anything else. Thank you. |
The variants missing from the output
Using the option --individual_zyg these should still be in the output. Can you try running vep again without extra options, something like this:
|
@dglemos I ran the command using the chr10.vep. HOMREF variants are present in the output. Does this mean there is a conflict with one of the plugins? |
Thanks for checking! Can you please try the following commands:
|
Hello. With only --individual_zyg I get 49509 lines in the VEP file |
Can you please send the output for |
Thank you for you continuing effort! --individual_zyg
--individual_zyg all --everything
--individual_zyg all + plugins
|
The variant is in all outputs with the correct value For the different number of lines, the option Output example without --everything:
Output example with --everything:
As you can see the last example has one more line because the variant overlaps a regulatory region. |
Thank you for your help. Unfortunately it doesn't solve my problem. The original run used --everything and plugins. The expectation was that adding '--individual_zyg all' would just add another field to the output. It does, but lines of output are missing. So, for some variants --individual_zyg must be causing some difference. |
I cannot reproduce the issue. Can you send an example of a variant with missing data or missing from the output?
Using this example, what are the counts when you run |
These are the tallies of the various run. The numbers are a little different from previous that included the header lines. I 'll need to get back to you on the first part. 49467 --individual_zyg all |
These counts look alright. |
Hello,
I have been using VEP V111 to annotated Freebayes VCF files. We have noticed that the ZYG field is missing from the output. Is this expected?
The command line for VEP was:
qsub -pe smp.pe 4 -V -cwd -N vep_fb_005SN_S25 -b y 'vep --offline --cache --dir_cache REDACTED_PATH/.conda/envs/VEP111/ --species homo_sapiens --dir_plugins REDACTED_PATH/.vep/Plugins/ --everything --tab --assembly GRCh38 -i 005SN_S25_hg38_freebayes136_MAPQ20_QUAL20_COV10_controls_subtracted.vcf.gz -o 005SN_S25_hg38_freebayes136_MAPQ20_QUAL20_COV10_controls_subtracted_v111.vep --force_overwrite --fork 4 --plugin AlphaMissense,file=REDACTED_PATH/.conda/envs/VEP111/AlphaMissense_data/AlphaMissense_hg38.tsv.gz --plugin CADD,snv=REDACTED_PATH/.conda/envs/VEP111/CADD_data/whole_genome_SNVs.tsv.gz,indels=REDACTED_PATH/.conda/envs/VEP111/CADD_data/gnomad.genomes.r4.0.indel.tsv.gz,force_annotate=1 --plugin gnomADc,REDACTED_PATH/.conda/envs/VEP111/gnomad_data/gnomad.ch.genomesv3.tabbed.tsv.gz --plugin REVEL,file=REDACTED_PATH/.conda/envs/VEP111/REVEL_data/new_tabbed_revel_grch38.tsv.gz --plugin SpliceAI,snv=REDACTED_PATH/.conda/envs/VEP111/spliceai_data/spliceai_scores.raw.snv.hg38.vcf.gz,indel=REDACTED_PATH/.conda/envs/VEP111/spliceai_data/spliceai_scores.raw.indel.hg38.vcf.gz'
An example of the VCF input follows.
Thank you,
Ian
The text was updated successfully, but these errors were encountered: