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

[Miguel Vazquez]

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 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 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 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 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 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 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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