bdgenomics.mango.genotypes.GenotypeSummary¶

class bdgenomics.mango.genotypes.GenotypeSummary(spark, ac, genotypeDataset, sample=1.0)[source]¶

GenotypeSummary class. GenotypeSummary provides visualizations for genotype based summaries.

__init__(spark, ac, genotypeDataset, sample=1.0)[source]¶

Initializes an GenotypeSummary class.

Args:

param genotypeDataset:
param spark:	SparkSession
param ac:	bdgenomics.adam.damContext.ADAMContext
	bdgenomics.adam.ds.GenotypeDataset
param sample:	fraction of reads to sample from

Methods

`__init__`(spark, ac, genotypeDataset[, sample])	Initializes an GenotypeSummary class.
`getGenotypeCallRatesDistribution`()	Computes a distribution of variant CallRate (called / total_variants) per sample
`getHetHomRatioDistribution`()	Computes a distribution of (Heterozygote/Homozygote) ratios per sample
`getVariantsPerSampleDistribution`()	Computes distribution of variant counts per sample.
`viewPileup`(contig, start, end[, reference, …])	Visualizes a portion of this GenotypeRDD in a scrollable pileup widget