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

Thu Jan 26 08:41:28 EST 2017

Hi all,

I can now confirm Miguel’s 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 Miguel’s reported previously (on DO52140)

I’ve 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, Miguel’s 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 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
M: +44 (0)7482 070730
E: jonas.demeulemeester at crick.ac.uk<%22mailto:>
W: www.crick.ac.uk<%22http://>

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:<NEUTRAL>

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.germline.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.germline.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>
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