[DOCKTESTERS] [DOCKTERTERS] 'pretty good' validation of Merge-Annotate for donor DO52621

[Miguel Vazquez]

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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