Today, I spent five hours at the Duke Medical employee orientation, which turned out to be un-relevant to me, who is not a health care providers 🙂 But, it was still very useful and helpful to get information about benefit, general safety, and medantory trainings.

Alarm set for signing up medical and other benefit within the first 60 days of employment.

Ok, talked to Joe, who is always helpful!

1. Get mapped linux drives from Windows (via Samba drive) from Qian, and Joe helped with the set up.
2. Met with Dongliang for advice. Accoring to Dongliang, David needs a solid and confident assessment on implementing the GATK into our existing pipeline with three primary questions (earlier page).
3. Will meet with Jessica for help again 🙂
4. Wanted to test whether Jessica’s script runs in my hands.
5. Talked to Jessica and got a lot of information!
6. Jessica will help: (1) get the allowable space for me to rerun (2) get BWA 0.4.9 pipeline scripts (3) will focus on dukscz0106 sample for the comparison purpose (4) first get ti/tv ratio tested!!!
7. Need to get read group informaiton from Ryan (he agrees to help out)

First pipeline run, yahoo! To evaluate ti/tv ratio for dukscz0106 sample
1. Script (gatk_titv_sam12_jl.sh) is located: /home/chavi/jl407/GATK-testing/workingDir/
2. Input bam file is: /nfs/chgv/seqanalysis2/ALIGNMENT/samples/dukscz0106/combined/combined_rmdup.bam
3. vcf file is: /home/chavi/jl407/GATK-testing/testRunJM/dukscz0106/vcf_snp_with_header_for_gatk
4. qsub gatk_titv_sam12_jl.sh