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View Code? Open in Web Editor NEWA pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
License: MIT License
A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
License: MIT License
Currently the filter used is minGQ, we should be using minQ too. This will make filtering with vcf2fasta redundant.
Add the annotation of called variants with SNPEff.
This will require either the creation of a local SNPEff database, or the use of reference sequences that are already included.
One of the processes failed with the error message:
Job 1949538.srvslshpc001 terminated as it used more cores (13.5) than requested (10).
Though it was resubmitted successfully, this may cause problems with larger datasets.
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