[DOCKTESTERS] Summary of validation of Dockers Sanger and DKFZ(+Delly)

Mon Feb 13 10:09:25 EST 2017

Thanks Matthias! That’s good, no action needed.
Best regards,
Junjun

On 2017-02-13, 9:04 AM, "Schlesner, Matthias"
<m.schlesner at Dkfz-Heidelberg.de> wrote:

>Hi Junjun,
>
>Please find attached some QC for DO51087. Except the very strong oxoG it
>has no striking problems. Some GC bias, but if we exclude on this
>something like 30% of the cohort would be out. And oxoG is well controlled
>by the Broad filter also in such strong cases. I think this donor could
>stay in.
>
>Best,
>Matthias
>
>
>Dr. Matthias Schlesner
>Division Theoretical Bioinformatics (B080)
>Head of Computational Oncology Group
>German Cancer Research Center (DKFZ)
>Foundation under Public Law
>Im Neuenheimer Feld 280
>69120 Heidelberg
>Germany
>office: Berliner Str. 41 (Mathematikon), room 02.MB.116
>phone: +49 6221 42-2720
>fax:      +49 6221 42-3626
>m.schlesner at dkfz.d <mailto:m.schlesner at dkfz.de>e
>www.dkfz.de <http://www.dkfz.de/>
> 
>Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>VAT-ID No.: DE143293537
>
>
>
>
>
>On 2/6/17, 4:24 PM, "Junjun Zhang" <Junjun.Zhang at oicr.on.ca> wrote:
>
>>Hi Matthias,
>>
>>Thanks for clarification.
>>
>>We had discussion about this donor (DO51087) during today¹s tech call.
>>Lincoln suggests to ask you to help viewing the QC metrics of this donor,
>>if appropriate, this donor may be added to the exclusion list.
>>
>>Just an FYI, you can find more information about this donor here:
>>https://docs.google.com/spreadsheets/d/126V4Dke1IvfVZqHLvZPUUeo7PO1Hi8jg8
>>Q
>>h
>>xiIDOFR4/edit#gid=1654136615 (search for DO51087).
>>
>>Can you please help with this?
>>
>>Thanks,
>>Junjun
>>
>>
>>
>>
>>On 2017-02-06, 1:28 AM, "Schlesner, Matthias"
>><m.schlesner at Dkfz-Heidelberg.de> wrote:
>>
>>>Hi Junjun,
>>>
>>>This sample has extreme OxoG which could  not be removed completely by
>>>our filter. Hence there is a huge number of artifacts remaining which
>>>blow up the file size.
>>>
>>>Best,
>>>Matthias
>>>
>>>
>>>Dr. Matthias Schlesner
>>>Division Theoretical Bioinformatics (B080)
>>>Head of Computational Oncology Group
>>>
>>>German Cancer Research Center (DKFZ)
>>>Foundation under Public Law
>>>Im Neuenheimer Feld 280
>>>69120 Heidelberg
>>>Germany
>>>office: Berliner Str. 41 (Mathematikon), room 02.MB.116
>>>phone: +49 6221 42-2720
>>>fax:      +49 6221 42-3626
>>>
>>>m.schlesner at dkfz.d<mailto:m.schlesner at dkfz.de>e
>>>www.dkfz.de<http://www.dkfz.de/>
>>>
>>> [unknown.png]
>>>
>>>Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>>>
>>>VAT-ID No.: DE143293537
>>>
>>>From: Junjun Zhang
>>><Junjun.Zhang at oicr.on.ca<mailto:Junjun.Zhang at oicr.on.ca>>
>>>Date: Monday, February 6, 2017 at 12:52 AM
>>>To: Jonas Demeulemeester
>>><Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.u
>>>k
>>>>
>>>>, Miguel Vazquez
>>>><miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>>
>>>Cc: "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>"
>>><docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>,
>>>"joachim.weischenfeldt at bric.ku.dk<mailto:joachim.weischenfeldt at bric.ku.d
>>>k
>>>>
>>>" 
>>><joachim.weischenfeldt at bric.ku.dk<mailto:joachim.weischenfeldt at bric.ku.d
>>>k
>>>>
>>>>, "Schlesner, Matthias"
>>>><m.schlesner at Dkfz-Heidelberg.de<mailto:m.schlesner at Dkfz-Heidelberg.de>>
>>>Subject: Re: [DOCKTESTERS] Summary of validation of Dockers Sanger and
>>>DKFZ(+Delly)
>>>
>>>Hi Miguel and Jonas,
>>>
>>>I hope DKFZ pipeline authors (cc¹d here) would be able to figure out the
>>>differences of the calls for DO52140
>>>
>>>Here I have another donor: DO51087. The size of the somatic SNV/MNV DKFZ
>>>call seems to be surprisingly large, the GZ¹d VCF file is greater than
>>>500MB. Here you can find more information about the file:
>>>https://dcc.icgc.org/repositories/files/FI500885. You can verify that in
>>>GNOS as well: 
>>>https://gtrepo-dkfz.annailabs.com/cghub/metadata/analysisFull/e1e9062e-3
>>>5
>>>e
>>>6-447d-bc61-591e76fbeee0.
>>>
>>>Matthias, can you please take a look of the VCF? Hope you may be able to
>>>spot something abnormal there.
>>>
>>>Maybe Miguel/Jonas, if you plan to test more donors for the DKFZ
>>>pipeline, can you please choose this donor? Tumour aligned BAM is:
>>>https://dcc.icgc.org/repositories/files/FI37278, normal aligned BAM is
>>>https://dcc.icgc.org/repositories/files/FI37277
>>>
>>>Thanks,
>>>Junjun
>>>
>>>
>>>
>>>From: 
>>><docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org<mailto:dockt
>>>e
>>>s
>>>ters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org>> on behalf of Jonas
>>>Demeulemeester 
>>><Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.u
>>>k
>>>>
>>>>
>>>Date: Saturday, February 4, 2017 at 10:14 AM
>>>To: Miguel Vazquez
>>><miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>>
>>>Cc: "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>"
>>><docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>
>>>Subject: Re: [DOCKTESTERS] Summary of validation of Dockers Sanger and
>>>DKFZ(+Delly)
>>>
>>>Hi Miguel,
>>>
>>>The comparison was indeed run largely using your scripts.
>>>I didn't notice any missteps but you never know of course.
>>>Hope they can pinpoint the issue.
>>>
>>>Cheers,
>>>Jonas
>>>
>>>
>>>On 3 Feb 2017, at 19:06, Miguel Vazquez
>>><miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:
>>>
>>>Excellent Jonas, this is very useful info.
>>>
>>> I guess you are using my own scripts for this. The possibility remains
>>>that there is a misstep in them regarding delly. Let's see what turns
>>>out
>>>of the checks by our friends at DKFZ.
>>>
>>>Best regards
>>>
>>>Have a great weekend
>>>
>>>Miguel
>>>
>>>On Feb 3, 2017 6:10 PM, "Jonas Demeulemeester"
>>><Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.u
>>>k
>>>>
>>>> wrote:
>>>Dear all,
>>>
>>>Also for the DKFZ (+Delly) workflow, I can confirm Miguel¹s results on
>>>samples DO52140 and DO50311.
>>>The dockerised pipelines return identical calls for SNV.MNVs and indels
>>>but partly different ones for SVs and CNVs, independent of the
>>>infrastructure.
>>>
>>>Best regards,
>>>Jonas
>>>
>>>
>>>
>>>
>>>
>>>RESULTS DO52140
>>>---------------
>>>
>>>Comparison of somatic.sv<http://somatic.sv> for DO52140 using DKFZ
>>>---
>>>Common: 72
>>>Extra: 23
>>>    - Example: 
>>>10:132840774:N:<DEL>,11:38252019:N:<TRA>,11:47700673:N:<TRA>
>>>Missing: 61
>>>    - Example: 
>>>10:134749140:N:<DEL>,11:179191:N:<TRA>,11:38252005:N:<TRA>
>>>
>>>
>>>Comparison of germline.sv<http://germline.sv> for DO52140 using DKFZ
>>>---
>>>Common: 1108
>>>Extra: 1116
>>>    - Example: 
>>>10:102158308:N:<DEL>,10:104645247:N:<DEL>,10:105097522:N:<DEL>
>>>Missing: 2908
>>>    - Example: 
>>>10:100107032:N:<TRA>,10:100107151:N:<TRA>,10:102158345:N:<DEL>
>>>
>>>
>>>Comparison of somatic.snv.mnv for DO52140 using DKFZ
>>>---
>>>Common: 37160
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.snv.mnv for DO52140 using DKFZ
>>>---
>>>Common: 3833896
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.indel for DO52140 using DKFZ
>>>---
>>>Common: 19347
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.indel for DO52140 using DKFZ
>>>---
>>>Common: 706572
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.cnv for DO52140 using DKFZ
>>>---
>>>Common: 275
>>>Extra: 94
>>>    - Example: 
>>>1:106505931:N:<LOH>,1:109068899:N:<DEL>,1:109359995:N:<DEL>
>>>Missing: 286
>>>    - Example: 10:88653561:N:<LOH>,11:179192:N:<LOH>,11:38252006:N:<LOH>
>>>
>>>
>>>
>>>
>>>RESULTS DO50311
>>>---------------
>>>
>>>Comparison of somatic.sv<http://somatic.sv> for DO50311 using DKFZ
>>>---
>>>Common: 231
>>>Extra: 44
>>>    - Example: 
>>>10:20596800:N:<TRA>,10:56066821:N:<TRA>,11:16776092:N:<TRA>
>>>Missing: 48
>>>    - Example: 
>>>10:119704959:N:<INV>,10:13116322:N:<TRA>,10:47063485:N:<TRA>
>>>
>>>
>>>Comparison of germline.sv<http://germline.sv> for DO50311 using DKFZ
>>>---
>>>Common: 1393
>>>Extra: 231
>>>    - Example: 
>>>10:134319313:N:<DEL>,10:134948976:N:<DEL>,10:19996638:N:<DEL>
>>>Missing: 615
>>>    - Example: 
>>>10:101851839:N:<TRA>,10:101851884:N:<TRA>,10:10745225:N:<DUP>
>>>
>>>
>>>Comparison of somatic.snv.mnv for DO50311 using DKFZ
>>>---
>>>Common: 51087
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.snv.mnv for DO50311 using DKFZ
>>>---
>>>Common: 3850992
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.indel for DO50311 using DKFZ
>>>---
>>>Common: 26469
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.indel for DO50311 using DKFZ
>>>---
>>>Common: 709060
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.cnv for DO50311 using DKFZ
>>>---
>>>Common: 731
>>>Extra: 213
>>>    - Example: 
>>>10:132510034:N:<DEL>,10:20596801:N:<NEUTRAL>,10:47674883:N:<NEUTRAL>
>>>Missing: 190
>>>    - Example: 
>>>10:100891940:N:<NEUTRAL>,10:104975905:N:<NEUTRAL>,10:119704960:N:<NEUTRA
>>>L
>>>>
>>>
>>>
>>>
>>>
>>>
>>>_________________________________
>>>Jonas Demeulemeester, PhD
>>>Postdoctoral Researcher
>>>The Francis Crick Institute
>>>1 Midland Road
>>>London
>>>NW1 1AT
>>>
>>>T: +44 (0)20 3796 2594<tel:+44%2020%203796%202594>
>>>M: +44 (0)7482 070730<tel:+44%207482%20070730>
>>>E: jonas.demeulemeester at crick.ac.uk
>>>W: www.crick.ac.uk
>>>
>>>
>>>
>>>On 26 Jan 2017, at 13:41, Jonas Demeulemeester
>>><Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.u
>>>k
>>>>
>>>> wrote:
>>>
>>>Hi all,
>>>
>>>I can now confirm Miguel¹s results with the Sanger workflow on donors
>>>DO50311 and DO52140.
>>>The calls made by the dockerised version are identical for Indels and
>>>SVs
>>>and produce only small discrepancies for SNV_MNVs and CNVs.
>>>The discrepancies seem independent of the system infrastructure as the
>>>number of missing/extra variants called are the same as Miguel¹s
>>>reported
>>>previously (on DO52140)
>>>
>>>I¹ve also updated the wiki page accordingly.
>>>
>>>Best regards,
>>>Jonas
>>>
>>>
>>>
>>>RESULTS - DO50311
>>>------
>>>
>>>
>>>Comparison of cnv for DO50311 using Sanger
>>>---
>>>Common: 138
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of indel for DO50311 using Sanger
>>>---
>>>Common: 812487
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of snv_mnv for DO50311 using Sanger
>>>---
>>>Common: 156313
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of sv for DO50311 using Sanger
>>>---
>>>Common: 260
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>
>>>
>>>
>>>RESULTS - DO52140
>>>------
>>>
>>>
>>>Comparison of cnv for DO52140 using Sanger
>>>---
>>>Common: 36
>>>Extra: 0
>>>Missing: 2
>>>    - Example: 10:11767915:T:<CNV>,10:11779907:G:<CNV>
>>>
>>>
>>>Comparison of indel for DO52140 using Sanger
>>>---
>>>Common: 803986
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of svn_mnv for DO52140 using Sanger
>>>---
>>>Common: 87234
>>>Extra: 5
>>>    - Example: 1:23719098:G,12:43715930:A,20:4058335:A
>>>Missing: 7
>>>    - Example: 10:6881937:T,1:148579866:G,11:9271589:A
>>>
>>>
>>>Comparison of sv for DO52140 using Sanger
>>>---
>>>Common: 6
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>
>>>
>>>
>>>
>>>For comparison, Miguel¹s report on DO51240:
>>>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
>>>
>>>
>>>_________________________________
>>>Jonas Demeulemeester, PhD
>>>Postdoctoral Researcher
>>>The Francis Crick Institute
>>>1 Midland Road
>>>London
>>>NW1 1AT
>>>
>>>T: +44 (0)20 3796 2594<tel:+44%2020%203796%202594>
>>>M: +44 (0)7482 070730<tel:+44%207482%20070730>
>>>E: jonas.demeulemeester at crick.ac.uk
>>>W: www.crick.ac.uk
>>>
>>>
>>>
>>>On 16 Jan 2017, at 14:24, Miguel Vazquez
>>><miguel.vazquez at cnio.es<mailto:miguel.vazquez at cnio.es>> wrote:
>>>
>>>Dear all,
>>>
>>>Let me summarize the status of the testing for Sanger and DKFZ. The
>>>validation has been run for two donors for each workflow: DO50311
>>>DO52140
>>>
>>>Sanger:
>>>----------
>>>
>>>Sanger call only somatic variants. The results are identical for Indels
>>>and SVs but almost identical for SNV.MNV and CNV. The discrepancies are
>>>reproducible (on the same machine at least), i.e. the same are found
>>>after running the workflow a second time.
>>>
>>>DKFZ:
>>>---------
>>>DKFZ cals somatic and germline variants, except germline CNVs. For both
>>>germline and somatic variants the results are identical for SNV.MNV and
>>>Indels but with large discrepancies for SV and CNV.
>>>
>>>
>>>Kortine Kleinheinz and Joachim Weischenfeldt are in the process of
>>>investigating this issue I believe.
>>>
>>>BWA-Mem failed for me and has also failed for Denis Yuen and Jonas
>>>Demeulemeester. Denis I believe is investigating this problem further. I
>>>haven't had the chance to investigate this much myself.
>>>
>>>Best
>>>
>>>Miguel
>>>
>>>
>>>
>>>
>>>---------------------
>>>RESULTS
>>>---------------------
>>>
>>>ubuntu at ip-10-253-35-14:~/DockerTest-Miguel$ cat results.txt
>>>
>>>Comparison of somatic.snv.mnv for DO50311 using DKFZ
>>>---
>>>Common: 51087
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.indel for DO50311 using DKFZ
>>>---
>>>Common: 26469
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.sv<http://somatic.sv/> for DO50311 using DKFZ
>>>---
>>>Common: 231
>>>Extra: 44
>>>    - Example: 
>>>10:20596800:N:<TRA>,10:56066821:N:<TRA>,11:16776092:N:<TRA>
>>>Missing: 48
>>>    - Example: 
>>>10:119704959:N:<INV>,10:13116322:N:<TRA>,10:47063485:N:<TRA>
>>>
>>>
>>>Comparison of somatic.cnv for DO50311 using DKFZ
>>>---
>>>Common: 731
>>>Extra: 213
>>>    - Example: 
>>>10:132510034:N:<DEL>,10:20596801:N:<NEUTRAL>,10:47674883:N:<NEUTRAL>
>>>Missing: 190
>>>    - Example: 
>>>10:100891940:N:<NEUTRAL>,10:104975905:N:<NEUTRAL>,10:119704960:N:<NEUTRA
>>>L
>>>>
>>>
>>>
>>>Comparison of germline.snv.mnv for DO50311 using DKFZ
>>>---
>>>Common: 3850992
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.indel for DO50311 using DKFZ
>>>---
>>>Common: 709060
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.sv<http://germline.sv/> for DO50311 using DKFZ
>>>---
>>>Common: 1393
>>>Extra: 231
>>>    - Example: 
>>>10:134319313:N:<DEL>,10:134948976:N:<DEL>,10:19996638:N:<DEL>
>>>Missing: 615
>>>    - Example: 
>>>10:101851839:N:<TRA>,10:101851884:N:<TRA>,10:10745225:N:<DUP>
>>>
>>>File not found 
>>>/mnt/1TB/work/DockerTest-Miguel/tests/DKFZ/DO50311//output//DO50311.germ
>>>l
>>>i
>>>ne.cnv.vcf.gz
>>>
>>>Comparison of somatic.snv.mnv for DO52140 using DKFZ
>>>---
>>>Common: 37160
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.indel for DO52140 using DKFZ
>>>---
>>>Common: 19347
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.sv<http://somatic.sv/> for DO52140 using DKFZ
>>>---
>>>Common: 72
>>>Extra: 23
>>>    - Example: 
>>>10:132840774:N:<DEL>,11:38252019:N:<TRA>,11:47700673:N:<TRA>
>>>Missing: 61
>>>    - Example: 
>>>10:134749140:N:<DEL>,11:179191:N:<TRA>,11:38252005:N:<TRA>
>>>
>>>
>>>Comparison of somatic.cnv for DO52140 using DKFZ
>>>---
>>>Common: 275
>>>Extra: 94
>>>    - Example: 
>>>1:106505931:N:<LOH>,1:109068899:N:<DEL>,1:109359995:N:<DEL>
>>>Missing: 286
>>>    - Example: 10:88653561:N:<LOH>,11:179192:N:<LOH>,11:38252006:N:<LOH>
>>>
>>>
>>>Comparison of germline.snv.mnv for DO52140 using DKFZ
>>>---
>>>Common: 3833896
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.indel for DO52140 using DKFZ
>>>---
>>>Common: 706572
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of germline.sv<http://germline.sv/> for DO52140 using DKFZ
>>>---
>>>Common: 1108
>>>Extra: 1116
>>>    - Example: 
>>>10:102158308:N:<DEL>,10:104645247:N:<DEL>,10:105097522:N:<DEL>
>>>Missing: 2908
>>>    - Example: 
>>>10:100107032:N:<TRA>,10:100107151:N:<TRA>,10:102158345:N:<DEL>
>>>
>>>File not found 
>>>/mnt/1TB/work/DockerTest-Miguel/tests/DKFZ/DO52140//output//DO52140.germ
>>>l
>>>i
>>>ne.cnv.vcf.gz
>>>
>>>Comparison of somatic.snv.mnv for DO50311 using Sanger
>>>---
>>>Common: 156299
>>>Extra: 1
>>>    - Example: Y:58885197:A:G
>>>Missing: 14
>>>    - Example: 1:102887902:A:T,1:143165228:C:G,16:87047601:A:C
>>>
>>>
>>>Comparison of somatic.indel for DO50311 using Sanger
>>>---
>>>Common: 812487
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.sv<http://somatic.sv/> for DO50311 using Sanger
>>>---
>>>Common: 260
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.cnv for DO50311 using Sanger
>>>---
>>>Common: 138
>>>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.indel for DO52140 using Sanger
>>>---
>>>Common: 803986
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.sv<http://somatic.sv/> for DO52140 using Sanger
>>>---
>>>Common: 6
>>>Extra: 0
>>>Missing: 0
>>>
>>>
>>>Comparison of somatic.cnv for DO52140 using Sanger
>>>---
>>>Common: 36
>>>Extra: 0
>>>Missing: 2
>>>    - Example: 10:11767915:T:<CNV>,10:11779907:G:<CNV>
>>>_______________________________________________
>>>docktesters mailing list
>>>docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>
>>>https://lists.icgc.org/mailman/listinfo/docktesters
>>>
>>>
>>>The Francis Crick Institute Limited is a registered charity in England
>>>and Wales no. 1140062 and a company registered in England and Wales no.
>>>06885462, with its registered office at 1 Midland Road London NW1 1AT
>>>
>>>_______________________________________________
>>>docktesters mailing list
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>>>https://lists.icgc.org/mailman/listinfo/docktesters
>>>
>>>
>>>The Francis Crick Institute Limited is a registered charity in England
>>>and Wales no. 1140062 and a company registered in England and Wales no.
>>>06885462, with its registered office at 1 Midland Road London NW1 1AT
>>>
>>>_______________________________________________
>>>docktesters mailing list
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>>>https://lists.icgc.org/mailman/listinfo/docktesters
>>>
>>>
>>>The Francis Crick Institute Limited is a registered charity in England
>>>and Wales no. 1140062 and a company registered in England and Wales no.
>>>06885462, with its registered office at 1 Midland Road London NW1 1AT
>>
>