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

[Denis Yuen]

Hi,


FYI I've also added Jonas's results from January 10th to https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data

(Not sure if Jonas can see this page)


________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org <docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org> on behalf of Miguel Vazquez <miguel.vazquez at cnio.es>
Sent: January 13, 2017 11:37 AM
To: Francis Ouellette
Cc: docktesters at lists.icgc.org
Subject: Re: [DOCKTESTERS] Sanger validation (DO52140) repeated: Same discrepancies

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<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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