cat-bgen fail
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Entering edit mode
4 weeks ago
lambard • 0

Hello community,

I had a bunch of vcf files that I converted from vcf file format to bgenix file format in order to compute Polyenic scores following this guideline https://2cjenn.github.io/PRS_Pipeline/#Extract_required_SNPs.

Now I have 22 bgen files for each autosomes and I need to concatenate them in a single file to follow the guide and perform downstream steps as QC...

but for some reason my command is interrupted :

cat-bgen -g /CECI/trsf/umons/biomemo/alambard/extract/*.bgen* -og /CECI/trsf/umons/biomemo/alambard/extract/initial_chr.bgen -clobber

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Abandon

I run bgenix 1.1.7 through conda container on a remote cluster and I have enough disk space. I have no idea of why this command doesn't work..

bgenix • 179 views
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