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Method Detail
Submitter Method Handle: EVA-GONL
Submitter Method ID: GATK
Submitted method description:
We used the GATK UG v1.6 for SNV discovery and calculation of genotype likelihoods. We ran GATK UG on 5Mb non-overlapping bins on all samples together. We applied the GATK UG multi-allelic model to call our SNVs to prevent wrongly calling multi-allelic si
odel is built using sites overlapping with known SNVs under the assumption that they are true polymorphic sites. The second model is built on the 3% least confident sites using them as true negatives. We used the following datasets and features to train t
ered the two following metrics and applied VQSR to the data afterwards: a) Sensitivity: proportion of sites in both GoNL and the training sets kept unfiltered. b) Specificity: Transition/Transversion (Ti/Tv) ratio in the entire dataset.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
EVA-GONL Frequency release_5 146
EVA-GONL Assay release_5 141