[DOCKTESTERS] [DOCKTERTERS] Update: Sanger also validated for Merge-Annotate -- 'pretty good' validation of Merge-Annotate for donor DO52621

[Miguel Vazquez]

Dear friends,

This is just a small update for the Merge-Annotate workflow. Last time I
skipped Sanger because I couldn't match some filenames. I've resolved that
issue and it validates perfectly. Below are the results now featuring the
Sanger workflow

Best

Miguel

---


Comparison of Merge-Annotate for DO52621 provider broad
---
Common: 2764
Extra: 0
Missing: 0


Comparison of Merge-Annotate for DO52621 provider dkfz
---
Common: 1953
Extra: 0
Missing: 0


Comparison of Merge-Annotate for DO52621 provider muse
---
Common: 5982
Extra: 3
    - Example:
* GL000193.1    94864   .       C       G       .       Tier4
SOMATIC;NormalEvidenceReads=0,0;NormalReads=14;TumourAvgVarBaseQ=35.0;TumourAvgVarMapQ=28.8;TumourAvgVarPosn=0.6;TumourEvidenceReads=5,0;TumourReads=35
GT:DP:AD:BQ:SS  0/1:35:30,5:28,30:2     0/0:14:14,0:29,0:.
* GL000195.1    150483  .       A       G       .       PASS
SOMATIC;NormalEvidenceReads=1,0;NormalReads=66;TumourAvgVarBaseQ=39.2;TumourAvgVarMapQ=10.8;TumourAvgVarPosn=0.56;TumourEvidenceReads=9,11;TumourReads=163
GT:DP:AD:BQ:SS  0/1:163:143,20:30,30:2  0/0:66:65,1:29,32:.
* GL000225.1    104343  .       C       A       .       Tier1
SOMATIC;NormalEvidenceReads=0,0;NormalReads=31;TumourAvgVarBaseQ=36.0;TumourAvgVarMapQ=44.17;TumourAvgVarPosn=0.38;TumourEvidenceReads=2,4;TumourReads=50
GT:DP:AD:BQ:SS  0/1:50:44,6:30,30:2     0/0:31:31,0:28,0:.
Missing: 3
    - Example:
* GL000193.1    94864   .       C       G       .       Tier4
SOMATIC;NormalEvidenceReads=0,0;NormalReads=14;TumourAvgVarBaseQ=35.0;TumourAvgVarMapQ=28.8;TumourAvgVarPosn=0.54;TumourEvidenceReads=5,0;TumourReads=35
GT:DP:AD:BQ:SS  0/1:35:30,5:28,30:2     0/0:14:14,0:29,0:.
* GL000195.1    150483  .       A       G       .       PASS
SOMATIC;NormalEvidenceReads=1,0;NormalReads=66;TumourAvgVarBaseQ=39.2;TumourAvgVarMapQ=10.8;TumourAvgVarPosn=0.57;TumourEvidenceReads=9,11;TumourReads=163
GT:DP:AD:BQ:SS  0/1:163:143,20:30,30:2  0/0:66:65,1:29,32:.
* GL000225.1    104343  .       C       A       .       Tier1
SOMATIC;NormalEvidenceReads=0,0;NormalReads=31;TumourAvgVarBaseQ=36.0;TumourAvgVarMapQ=44.17;TumourAvgVarPosn=0.42;TumourEvidenceReads=2,4;TumourReads=50
GT:DP:AD:BQ:SS  0/1:50:44,6:30,30:2     0/0:31:31,0:28,0:.


Comparison of Merge-Annotate for DO52621 provider sanger
---
Common: 1615
Extra: 0
Missing: 0


On Fri, May 5, 2017 at 5:53 PM, Miguel Vazquez <mikisvaz at gmail.com> wrote:

> Dear all,
>
> I've completed the validation for Merge-Annotate. The results for the SNV
> providers Broad and DKFZ is a perfect match, and for Muse there are only 3
> small discrepancies (see below).
>
> For Sanger there is something odd. There is a file for the annotated VCF
> but not for the non-annotated, instead there is a file called SVCP. Are
> these equivalent:
>
> fc876f51-0577-3b53-e040-11ac0d48515e_annotated_*sanger*_SNV.vcf.gz
> fc876f51-0577-3b53-e040-11ac0d48515e.*svcp*_1-0-3.
> 20150102.somatic.snv_mnv.pass-filtered.oxoG.vcf.gz
>
> Best regards
>
> Miguel
>
> ----RESULTS-----
>
>
> Comparison of Merge-Annotate for DO52621 provider broad
> ---
> Common: 2764
> Extra: 0
> Missing: 0
>
>
> Comparison of Merge-Annotate for DO52621 provider dkfz
> ---
> Common: 1953
> Extra: 0
> Missing: 0
>
>
> Comparison of Merge-Annotate for DO52621 provider muse
> ---
> Common: 5982
> Extra: 3
>     - Example:
> * GL000193.1    94864   .       C       G       .       Tier4
> SOMATIC;NormalEvidenceReads=0,0;NormalReads=14;TumourAvgVarBaseQ=35.0;
> TumourAvgVarMapQ=28.8;TumourAvgVarPosn=*0.6*;TumourEvidenceReads=5,0;TumourReads=35
> GT:DP:AD:BQ:SS  0/1:35:30,5:28,30:2     0/0:14:14,0:29,0:.
> * GL000195.1    150483  .       A       G       .       PASS
> SOMATIC;NormalEvidenceReads=1,0;NormalReads=66;TumourAvgVarBaseQ=39.2;
> TumourAvgVarMapQ=10.8;TumourAvgVarPosn=*0.56*;TumourEvidenceReads=9,11;TumourReads=163
> GT:DP:AD:BQ:SS  0/1:163:143,20:30,30:2  0/0:66:65,1:29,32:.
> * GL000225.1    104343  .       C       A       .       Tier1
> SOMATIC;NormalEvidenceReads=0,0;NormalReads=31;TumourAvgVarBaseQ=36.0;
> TumourAvgVarMapQ=44.17;TumourAvgVarPosn=*0.38*;TumourEvidenceReads=2,4;TumourReads=50
> GT:DP:AD:BQ:SS  0/1:50:44,6:30,30:2     0/0:31:31,0:28,0:.
> Missing: 3
>     - Example:
> * GL000193.1    94864   .       C       G       .       Tier4
> SOMATIC;NormalEvidenceReads=0,0;NormalReads=14;TumourAvgVarBaseQ=35.0;
> TumourAvgVarMapQ=28.8;TumourAvgVarPosn=*0.54*;TumourEvidenceReads=5,0;TumourReads=35
> GT:DP:AD:BQ:SS  0/1:35:30,5:28,30:2     0/0:14:14,0:29,0:.
> * GL000195.1    150483  .       A       G       .       PASS
> SOMATIC;NormalEvidenceReads=1,0;NormalReads=66;TumourAvgVarBaseQ=39.2;
> TumourAvgVarMapQ=10.8;TumourAvgVarPosn=*0.57*;TumourEvidenceReads=9,11;TumourReads=163
> GT:DP:AD:BQ:SS  0/1:163:143,20:30,30:2  0/0:66:65,1:29,32:.
> * GL000225.1    104343  .       C       A       .       Tier1
> SOMATIC;NormalEvidenceReads=0,0;NormalReads=31;TumourAvgVarBaseQ=36.0;
> TumourAvgVarMapQ=44.17;TumourAvgVarPosn=*0.42*;TumourEvidenceReads=2,4;TumourReads=50
> GT:DP:AD:BQ:SS  0/1:50:44,6:30,30:2     0/0:31:31,0:28,0:.
>
>
>
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