Dennis Hendriksen

Hi @yougulianren, The error you are running into is triggered in a workaround for Ensembl VEP affecting only short tandem repeat variants. What is you ARG_MAX? For modern linux distributions...

You could try disabling the line `args+=("--pubmed")` in `modules/vcf/templates/annotate.sh`, at a first glance this seems to be responsible for a significant amount of characters.

That is unfortunate, the example you provided should go down from 560K characters to 183K characters after applying the pubmed workaround. Could you confirm that is the case?

Hello @yougulianren, Thank you for sharing your data. I can reproduce your issue and can confirm that disabling the line `args+=("--pubmed")` does not resolve the issue. I did find another...

Hello @moskalenko, could it be that ExpansionHunter uses samtools under the hood and you are running into the same issue as https://github.com/HKU-BAL/Clair3/issues/180? In that case setting the environment variable `REF_PATH=:`...

Unfortunately not, I'll report back once the issue occurs again.