Nalini Ganapati
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Recent activity by Nalini Ganapati Sort by recent activity-
Enrico Cocchi, we are not able to reproduce the issue. We do not get the [E::vcf_parse_format] errors and genomicsdb seems to be correctly generated. ./gatk --java-options '-DGATK_STACKTRACE_ON_U...
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Hello Enrico Cocchi, would it be possible to include a small vcf file highlighting the issue?
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Thanks Lucas Taniguti. Let me know how it performs with larger datasets.
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As before, after downloading the new library, please use your command as before - GOOGLE_APPLICATION_CREDENTIALS=/home/my/secret.json $GATK --java-options "-Dgenomicsdb.library.path=/home/taniguti/...
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Lucas Taniguti I have placed another library here.This library tries a few well known paths on Linux machines, You could try that if you like, there will be some debugging statements like `CA Certs...
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Here is the link to the genomicsdb library. After downloading, here is a sample command for invoking gatk by pointing to the directory of the library - ./gatk-4.1.9.0/gatk --java-options "-Dgenomi...
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Hello Lucas Taniguti, I have a solution for the GCS issue. Just wondering if you could quickly try it out if I send you the native genomicsdb library with instructions to run it with gatk and java-...