[DOCKTESTERS] Sanger 2º validation (DO52140): Very small discrepancies

[Francis Ouellette]

The question that we should answer once is:

Are differences we see in the output from a given pipeline (how ever small they are) cause
by randomness (stochastic) or are they because of the way we are running it.

So if you run the same pipeline twice, and do or do not get the same answer (8 or
10 differences, as you have seen), are you able to reproduce that, or will always be
different each time you run it.

We don’t need to do that for all pipelines that generate different results, but maybe
once, so that when Lincoln asks “is this difference stochastic or reproducible?” I can
say something better than what I said last time, which was “Stochastic, is my
educated guess”  :-)

@bffo



On Dec 27, 2016, at 13:16, Miguel Vazquez <miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:

Francis,

This was on a new donor. I decided to get a second donor  before repeating the first. The first  donor also had differences in SNVs, but no differences in CNV.

Since the discrepancies for the first donor were not deemed too critical, I've actually moved onto trying the bwa-mem workflow, which I couldn't make to run on test data and so I'm trying on real data.  Should I instead try a second run on a donor to test if the differences are the same?

Best

Miguel

On Dec 27, 2016 5:30 PM, "Francis Ouellette" <francis at oicr.on.ca<mailto:francis at oicr.on.ca>> wrote:

Are the differences the same or different then the last time you ran this?
Was this Sanger workflow run on the same infrastructure as the last
one you did?

@bffo



On Dec 27, 2016, at 08:24, Miguel Vazquez <miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:

Dear all,

The test for the Sanger workflow on the second sample is complete. The results are posted below.

In brief, somatic indels and SV are a 100% match (803986 and 6 respectively matches) there are small differences in somatic.snv.mnv (+5 -7 with 87234 matches) and somatic.cnv (-2 and 36 matches)

Best regards

Report
~~~~~~

Comparison of somatic.cnv for DO52140 using Sanger
---
Common: 36
Extra: 0
Missing: 2
    - Example: 10:11767915:T:<CNV>,10:11779907:G:<CNV>


Comparison of somatic.indel for DO52140 using Sanger
---
Common: 803986
Extra: 0
Missing: 0


Comparison of somatic.snv.mnv for DO52140 using Sanger
---
Common: 87234
Extra: 5
    - Example: 1:23719098:A:G,12:43715930:T:A,20:4058335:T:A
Missing: 7
    - Example: 10:6881937:A:T,1:148579866:A:G,11:9271589:T:A


Comparison of somatic.sv<http://somatic.sv/> for DO52140 using Sanger
---
Common: 6
Extra: 0
Missing: 0


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