Sprint meeting 2016 11 15

Sprint meeting 2016 11 15 9.00-10.00, Uppsala BMC Navet, E10:2309 or video

Virtual meeting room: SciLifeLab@vconf.kth.se ; Pinkod: 8800; Rumsnummer: 990 SIP/H323: connect to SciLifeLab@vconf.kth.se. Web browser: https://vconf.kth.se/. Set SciLifeLab as conference room and ad your name below

Note: Irma has been down so the WF is not yet run on the SweRef cohort.

Goals

• Implement feature: Histogram filtering in WF (Pall -> Johan)

• Create dummy tracks to test filtering. Done!

• Run: WF with Manta on SweRef on Irma (Johan -> Francesco)

• Testruns done, but crashed. Unclear if it was a problem with WF or a problem with the cluster. Cluster has then been down so no more test are done.

• Feature: Multiple bam-files in paralell. Done! (Avoids multiple NextFlow sessions)

• Implement process: To go from histogram bed-tracks to visualize in SweRef Exac browser (Pall to provide Daniel with dummy tracks)

• Create dummy tracks for visualization (same as above). Done.

• Visualize in SweRef ExAC browser. Björn talk to Daniel.

• Add: Create histogram coverage track also. (Pall -> Daniel)

• Finish implementation of TIDDIT + CNVnator.

• Status: Not done.

• Benchmarking: Add GenomeSTRIP calls to Palls benchmarking stats. Find out what can be done with the GenomeSTRIP genotyping module. (Pall, sync with Anna/Jin)

• Testrun GenomeSTRIP on Irma with 20-30 samples (1 sample failed).

Tried successfully: First step worked. Installed so that GenomeSTRIP can work with SLURM. So this is great! Pall to testrun the other steps too.

• Pall will quit at the bioinfo platform and move back to Island, last day Dec 9. Björn to sort out staff to take over in November.

• Not decided yet.