[DOCKTESTERS] Sanger validation (DO52140) repeated: Same discrepancies

[Miguel Vazquez]

Hi all,

I've completed a second run of the Sanger pipeline for donor DO52140 and
have obtained the *same discrepancies* as detailed below.

Jonas from Crick has agreed to repeat one of the donors I have ran in his
infrastructure to see if the discrepancies are dependent on the setup.

Best regards

Miguel

On Tue, Dec 27, 2016 at 7:16 PM, Miguel Vazquez <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> 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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