GATK: Variant Quality Score Recalibration

(howto) Apply hard filters to a call set

Genome-Wide Linkage, Exome Sequencing and Functional Analyses Identify ABCB6 as the Pathogenic Gene of Dyschromatosis Universalis Hereditaria (a VQSR applied example)

What VQSR training sets / arguments should I use for my specific project? (QP is not recommended for the Exome-sequencing pipeline).

What does inbreedingCoeff mean?  (In relation to GATK)

Pedigree Analysis (Note that you will need at least 10 founders to compute the inbreeding coefficient.)

Variant Quality Score Recalibration (Broad Institute)

Call variations using the GATK Haplotype Caller workflow  (For Variant Quality Recalibration)

Intraclonal heterogeneity and distinct molecular mechanisms characterize the progression of t(4;14) and t(11;14) myeloma (Explanations of tranches and variant quality score recalibration).

variant calling, quality score recalibration, evaluation and filtering

Variant calling by Simon Rasmussen, 2013