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Problem with the moltenize version of the GenotypeConcordance

thondeboerthondeboer Redwood City, CA, USAMember ✭✭

Hi,

I ran GentoypeConcordance in the moltenize mode and it seems that the Comp_Genotype column has the incorrect value.....
It seems the Comp_Genotype contains the same text as the Eval_Genotype rather than the correct comparison...
So there are three HET/HET lines, while they should be HET/HET, HET/HOM_REF, HET/HOM_VAR (I am guessing form the non-moltenized version)

See below...


#:GATKReport.v1.1:5
#:GATKTable:4:38:%s:%s:%s:%.3f:;
#:GATKTable:GenotypeConcordance_CompProportions:Per-sample concordance tables: proportions of genotypes called in comp
Sample Eval_Genotype Comp_Genotype Proportion
A73U04UT9 HET HET 0.036
A73U04UT9 HET HET 0.000
A73U04UT9 HET HET 0.000
A73U04UT9 HOM_REF HOM_REF 0.005
A73U04UT9 HOM_REF HOM_REF 0.040
A73U04UT9 HOM_REF HOM_REF 0.000
A73U04UT9 HOM_VAR HOM_VAR 0.005
A73U04UT9 HOM_VAR HOM_VAR 0.000
A73U04UT9 HOM_VAR HOM_VAR 0.045
.
.
.
Thon

Answers

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