# Package picard.arrays

- Class Summary
  Class | Description
  --- | ---
  BafRegressMetrics |
  CollectArraysVariantCallingMetrics | Collects summary and per-sample metrics about variant calls in a VCF file.
  CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics |
  CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics |
  CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics |
  CombineGenotypingArrayVcfs | A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
  CreateBafRegressMetricsFile | A simple program to create a standard picard metrics file from the output of bafRegress
  CreateVerifyIDIntensityContaminationMetricsFile | A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
  GtcToVcf | Class to convert an Illumina GTC file into a VCF file.
  MergePedIntoVcf | Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
  VcfToAdpc | A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
  VerifyIDIntensityContaminationMetrics |