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- Finalized Second set of data to run for variant calling for Day 1 Afternoon to show biologically relevant mutations. Data: PCMP_H326 and PCMP_H434
- Remove running individual variant calling commands and run each steps as a shell/pbs script. Run this shell script before lunch. Create variant calling shell script and mention in course website
- Organize results of Variant calling steps in different steps folder.
- Add a flow chart summarizing each steps of Variant calling.
- Add variant calling and IGV exercise for PCMP_H326
- Add IGV to website and get rid of Artemis
- Extract basic and important variant annotation information from snpEff annotated vcf file. Script to parse snpeff annotation into a table
- Make sure the KPNIH1 genbank file has the MgrB annotation.
- Change VRE example to something simpler.
Colistin resistance in Acinetobacter? what are we looking at?
- Update instructions for exercise at the end (e.g. not running steps of pipeline, but instead seeking information from output files). vcf and alignment files exploration. SAM file exploration.
- Add gene name/product name in snpeff parser.
The text was updated successfully, but these errors were encountered:
Colistin resistance in Acinetobacter? what are we looking at?
The text was updated successfully, but these errors were encountered: