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

[Miguel Vazquez]

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> 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> 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 for DO52140 using Sanger
---
Common: 6
Extra: 0
Missing: 0



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