Error while annotating multi sample VCF about open-cravat HOT 16 CLOSED

Thanks. I'm testing on my system now. I'll get back to you after the test.

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The errors with the mapper have been fixed. Please do oc module install hg38 -v 1.9.8 to install the fixed mapper.

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The fixed version of mavedb (1.0.1), metalr (1.0.2), and swissprot_ptm (1.0.1) have been published. With these, I think that the only remaining issue is the one related to alternate chromosomes. We'll check and get back to you.

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No! Thank you very much for you quick response! Keep up the good work!

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Hi, thanks for letting us know. some variants were not properly handled by the hg38 mapper. I'll take a look. Regarding the error with clinvar, can you check with oc module install clinvar ? It may be that the data for the clinvar module is not properly installed. Regarding the last exception, it will be fixed in the next release (open-cravat 2.1.3), but if you prefer you can patch yourself for now: do pip list -v | grep cravat to know the location of the site-packages folder for your Python. Then, that folder/cravat/inout.py should be replaced with the file of the same name at https://github.com/KarchinLab/open-cravat/blob/2.1.3/cravat/inout.py.

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Q1: Can I use an already annotated VCF (e.g. EXAC, Clinvar) file with openCravat?

Q2:

kokyriakidis@XAROS-WORKSTATION:~/Desktop$ oc module install clinvar
clinvar: latest is already installed. (2020.02.11.1)
No modules to install found

EDIT:
After the patch the job finished succesfully. Here is the new log.
log2.txt

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Yes, you can use already annotated VCF. The annotation fields in the INFO column will be transferred to the result of oc run, under "Extra VCF Info" group.

Regarging clinvar, can you show me the result of oc module ls clinvar ? The size of the module should be 115.3MB. If not, oc module install clinvar -f -d will force re-installing the module.

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kokyriakidis@XAROS-WORKSTATION:/media/kokyriakidis/PRODUCTION/ADHD/work$ oc module ls clinvar
Name Title Type Version Data source ver Size
clinvar ClinVar annotator 2020.02.11.1 2020.02.11 115.3 MB

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I reinstalled it but no change
log3.txt

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Here is a log using many annotators. Many tracebacks occure
log4.txt

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Can you share the .err file also? On my system, clinvar went fine and .err file can reveal more about what happened.

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ADHD-gatk-haplotype-annotated.vcf.zip
ADHD-gatk-haplotype-annotated.vcf.log

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Thanks. The errors from the annotation modules (clinvar, metasvm, and etc) were because their data does not cover the alternate chromosomes. We try to faithfully transfer original annotation data, so most likely the source data does not have these alternate chromosomes, but we will take a look again. The errors from the mapper are mostly fixed. I'll publish a new mapper for you to use soon.

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Thank you so much for your support!

I will wait!

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A fixed version of hg19 module has been published (v1.0.6). oc module install hg19 -v 1.0.6 to get it.

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We have just verified that the source data of those annotation modules does not have the alternate chromosomes which produced exceptions in your job. The next version of open-cravat, 2.1.3, will handle it better so that something else than no such table exception will show on the log file.

I think that this concludes the investigation and fix, but is there any remaining issue?

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