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

[Christina Yung]

Hi Folks,

Here are the instructions for preparing the data as input to BWA-Mem.  
If you use a different protocol, please share.

https://wiki.oicr.on.ca/display/PANCANCER/Preparing+paired-end+data+for+upload

Christina


On 17-01-16 09:24 AM, Miguel Vazquez 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>
>
>
> This body part will be downloaded on demand.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.icgc.org/mailman/private/docktesters/attachments/20170116/79d87a62/attachment-0001.html>