Sprint meeting 2016 10 24

Monday 2016-10-24, 9.00-ca 10.30

E10:3309, BMC, Navet, Uppsala or video.

Virtual meeting room: SciLifeLab@vconf.kth.se ; Pinkod: 8800; Rumsnummer: 9909

SIP/H323: connect to SciLifeLab@vconf.kth.se.

Web browser: https://vconf.kth.se/. Set SciLifeLab as conference room and ad your name below

We will go through the goals below. Much of this might remain since both Pall and Johan have been heavily involved in the SweGen 1000 genomes release (which had high priority, https://swefreq.nbis.se/#/).

Goals

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

• First create tracks from SweGen 1000 genomes.

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

• Needs to testrun on Irma to give feedback to Johan //Björn+ Johan to talk to NGI (Johan D?)

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

• Status: Still to do.

• Finish implementation of TIDDIT + CNVnator.

• Status: Still to do

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

• Pall got some info from Jin. Installation works on test data. Tried on singe bam files but failed. Might need 20-30 samples per run. Pall to use test sample from another project to see if it can run. (Hours logged on the ToolBox project)

• 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.

Note: Interesting paper The Genome of the Netherlands Consortium: http://www.nature.com/articles/ncomms12989