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GitHub for the SIB courses NGS - Genome variant analysis
Home Page: https://sib-swiss.github.io/NGS-variants-training/
License: Creative Commons Attribution 4.0 International
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ngs-variants-training's Issues
Explain the concept of optical duplicates (i.e. one spot called as multiple). Is implemented in picard and samtools markdup
.
the variant calling chapter takes long. It's probably best to break it up, or move parts to other chapters. For example BQSR to the alignment chapter?
Helps to reduce differences between participants, and increases time for 'important' topics.
Now at /opt/conda/share/snpeff-5.0-1
, which used to be a directory in the jupyter container
Frees time during the course.
E.g. in the sequencing - alignment presentation.
We use --select-type
for gatk SelectVariants
, but according to the docs it should be --select-type-to-include