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VCCRI / VPOT

VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files.
GNU General Public License v3.0
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VPOT convertVEP #7

Open itsmestewart opened 2 months ago

itsmestewart commented 2 months ago

Hello there,

My file was annotated using VEP, and I am trying to convert the annotated VEP output to a format accepted by VPOT.py using these commands:

python3 ../VPOT_6_1_convertVEP.py utility input.VEP.vcf out.vep_convert.vcf python3 ../VPOT.py utility input.VEP.vcf out.vep_convert.vcf What I wonder is that there is no output and no error message.

I did the same with test data. Initially, the conversion was successful, but when I tried for the second time, no output and no error were observed. python3 ../VPOT_6_1_convertVEP.py utility test_vep_original.vcf test.vcf

I tried to run VPOT.py prioritize, it was running fine and i could see the output.

Also using this comd as advised in README.file does not work

python3 ../VPOT.py utility convertVEP merge test_vep_original.vcf test_vep_converted.vcf

Could you please advise how to successfully use VPOT for VEP-annotated file conversion?

eipVCCRI commented 2 months ago

Hi there,

VEP annotation output is always tricky to work with, as they have so many annotation variables.

If it is possible, can you send/attach a small sample of your VCF for me to test with? Or else try using a small sample of your VCF to test yourself.

Thanks. Eddie