[DOCKTESTERS] Sanger pipeline completed, small discrepancies with GNOS VCF (99.9905% accuracy)

[Francis Ouellette]

Miguel,

I personally think this is a slippery slope, but the PCAWG-tech (i.e. Lincoln and Christina) asked
if you could repeat this experiment, and see if you get the same different variants, or the same,
and in particular, do you think the minor differences you see are caused by the cloud
infrastructure you are using.

Would be good to test for that too.

Can you redo before Monday’s call?

@bffo


--
B.F. Francis Ouellette          http://oicr.on.ca/person/francis-ouellette








On Dec 5, 2016, at 7:41 AM, Miguel Vazquez <miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:

Dear all,

The Sanger pipeline completed, after about 2 weeks of computing, for donor DO50311

The results are the following:

Comparison for DO50311 using Sanger
---
Common: 156299
Extra: 1
    - Example: Y:58885197:G
Missing: 14
    - Example: 1:102887902:T,1:143165228:G,16:87047601:C


The donor results for DKFZ yielded

Comparison for DO50311 using DKFZ
---
Common: 51087
Extra: 0
Missing: 0


In both cases I'm comparing agains the VCF file downloaded from GNOS. I've updated the information here

https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data


Best regards

Miguel


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