[x] - 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
[x] - 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
[x] - Organize results of Variant calling steps in different steps folder.
[ ] - Add a flow chart summarizing each steps of Variant calling.
[x] - Add variant calling and IGV exercise for PCMP_H326
[x] - Add IGV to website and get rid of Artemis
[x] - Extract basic and important variant annotation information from snpEff annotated vcf file. Script to parse snpeff annotation into a table
[x] - 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.