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AlphaMissense_hg38.tsv.gz tabix indexing issue VEP

Hi! I'm experiencing the issue with the tabix indexing of AlphaMissense_hg38.tsv.gz file. I've installed alphamissense plugin in VEP and have downloaded the requested files and launch the tabix command before use it. The error tells me that it can not be indexed directly because the file is not BGZIP compressed. The file is gzipped with x-gzip aplication. Therefore, I tried to unzip it using gzip -dc command in order to perform BGZIP compression but it tells me that the file not in gzip format. From some explanations of diffrence between gzip and x-gzip formats seems that they are equivalent. Any suggestions and ideas how to solve this issue?

plugin vep alphamissence
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written by Katsiaryna • Katsiaryna

1 answer

IIRC it's already compressed with bgzip. You can just index with tabix.

wget https://storage.googleapis.com/dm_alphamissense/AlphaMissense_hg38.tsv.gz # re download the data
tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz # index with tabix
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written by barslmn • barslmn

Thanks for your reply. For indexing in cluster I used tabix Singularity image tabix_v0.2.6.sif. The command I have been using is: singularity exec tabix_v0.2.6.sif tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz I get the error of command run:

INFO:    Converting SIF file to temporary sandbox...
open: No such file or directory
[tabix] was bgzip used to compress this file? AlphaMissense_hg38.tsv.gz
INFO:    Cleaning up image...

It seems that it doesn't recognize this file?

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written by Katsiaryna • Katsiaryna

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