Reads2Ref
cli
Reads2RefArgs
cli
readInput
MpileupArgs
PileupAggregatorArgs
Reads2RefArgs
reads
Fasta2ADAMArgs
recalibrateBaseQualities
TransformArgs
recurse1
CompareADAMArgs
FindReadsArgs
recurse2
CompareADAMArgs
FindReadsArgs
repartition
SparkArgs
run
ADAM2Vcf
ADAMSparkCommand
Bam2ADAM
BuildInformation
CalculateDepth
CompareADAM
Fasta2ADAM
FindReads
FlagStat
GenotypeConcordance
ListDict
MpileupCommand
PileupAggregator
PluginExecutor
PrintADAM
PrintTags
Reads2Ref
SummarizeGenotypes
Transform
Vcf2ADAM
VcfAnnotation2ADAM