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diskin-lab-chop / AutoGVP

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Script missing #249

Closed nandobonf closed 5 months ago

nandobonf commented 5 months ago

Dear authors, I am trying to implement autoGVP in my pipeline, however, following the user guide at point 5: python autoPVS1_from_VEP_vcf.py --genome_version hg38 --vep_vcf test_VEP.vcf > test_autopvs1.txt

It is not clear to me where the "autoPVS1_from_VEP_vcf.py" script is located. I do not see it available from the autoPVS1 page. Is it something you customized? If yes, could you please share it? Thanks in advance.

jharenza commented 5 months ago

Hi @nandobonf - thank you for bringing this to our attention. We indeed did customize AutoPVS1 to remove hg19 files, lift over the gene symbols to be consistent with VEP 105, and select specific transcripts based on rank. Here is the version we had used in the manuscript, with the specific script of interest here.

We will try to update our documentation here to clarify, but please let us know if you have any further questions.

jharenza commented 5 months ago

The dockerfile for this version is:

docker pull pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v2.0.0
nandobonf commented 5 months ago

Ok thanks for your feedback, that helps a lot. Wrt VEP, do I need to use the v104 as from the guidelines or the v105 as you write?

jharenza commented 5 months ago

You can use whatever you would like, however if using anything other than 104 as we did, we recommend lifting gene symbols in the PVS1.level file of AutoPVS1 from 104 to that version. We have the new file available in our AutoPVS1 version, so totally up to you.

jharenza commented 5 months ago

Hi @nandobonf - I have updated the user guide to recommend using D3b AutoPVS1 to avoid confusion, and updated the link. Thank you for pointing it out. Will close this, but feel free to open an issue if you need anything else.