org.hammerlab.guacamole.variants
Arguments that callers can include to support concordance calculations.
Evaluate a set of called genotypes by computing precision, recall and F1-Score
Evaluate a set of called genotypes by computing precision, recall and F1-Score
Precision = Correct Calls / All Calls Made = Correct Calls / (Correct Calls + Incorrect Calls) Recall = Correct Calls / All True Variants = Correct Calls / (Correct Calls + Incorrect Omissions)
F1-Score = 2 * (Precision * Recall) / (Precision + Recall)
All three metrics range from 0 to 1, where 1 would be perfect.
Genotypes to test
Known-set of validated genotypes
true if want to exclude single nucleotides polymorphism in the evaluation (default: false)
true if want to exclude insertions in the evaluation in the evaluation (default: true)
name of a chromosome, if any, to filter to (default: null)
precision, recall and f1score
Load genotypes from ADAM Parquet or VCF file
Load genotypes from ADAM Parquet or VCF file
path to VCF or ADAM genotypes
spark context
RDD of ADAM Genotypes
Evaluate a set of called genotypes and print precision, recall and F1-Score
Evaluate a set of called genotypes and print precision, recall and F1-Score
parsed arguments
ADAM genotypes (i.e. the variants)
spark context
As a convenience to users experimenting with different callers, some variant callers include functionality to compare the called variants to a gold standard VCF after they are computed, in the same job. We implement that logic here.