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

Fri Feb 3 13:05:57 EST 2017

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> wrote:

> Dear all,
>
> Also for the DKFZ (+Delly) workflow, I can confirm Miguel’s 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 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 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 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 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:<NEUTRAL>
>
>
>
>
>
> _________________________________
> Jonas Demeulemeester, PhD
> Postdoctoral Researcher
> The Francis Crick Institute
> 1 Midland Road
> London
> NW1 1AT
>
> *T:* +44 (0)20 3796 2594 <+44%2020%203796%202594>
> M: +44 (0)7482 070730 <+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> wrote:
>
> 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 <+44%2020%203796%202594>
> M: +44 (0)7482 070730 <+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> 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 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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>
> 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
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