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Day 1 Afternoon #49

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7 of 11 tasks
alipirani88 opened this issue Feb 14, 2019 · 0 comments
Open
7 of 11 tasks

Day 1 Afternoon #49

alipirani88 opened this issue Feb 14, 2019 · 0 comments

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@alipirani88
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alipirani88 commented Feb 14, 2019

  • - 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.
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