Add Metric Outputs

[dansteiert]

There are already some Alignment Metrices, what about offering additional metrices from the GATK framework:

•  CollectAlignmentSummaryMetrics (Picard)      <b>Produces a summary of alignment metrics from a SAM or BAM file.</b>
  

•   CollectBaseDistributionByCycle (Picard)      Chart the nucleotide distribution per cycle in a SAM or BAM file
  

•   CollectGcBiasMetrics (Picard)                Collect metrics regarding GC bias.
  

•   CollectHsMetrics (Picard)                    Collects hybrid-selection (HS) metrics for a SAM or BAM file. -> already implemented
  

•   CollectInsertSizeMetrics (Picard)            Collect metrics about the insert size distribution of a paired-end library. - already implemented
  

•   CollectJumpingLibraryMetrics (Picard)        Collect jumping library metrics.
  

•   CollectOxoGMetrics (Picard)                  Collect metrics to assess oxidative artifacts.
  

•   CollectQualityYieldMetrics (Picard)          Collect metrics about reads that pass quality thresholds and Illumina-specific filters.
  

•   CollectRawWgsMetrics (Picard)                Collect whole genome sequencing-related metrics.
  

•   CollectRnaSeqMetrics (Picard)                Produces RNA alignment metrics for a SAM or BAM file.
  

•   CollectRrbsMetrics (Picard)                  <b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b>
  

•  CollectSamErrorMetrics (Picard)              Program to collect error metrics on bases stratified in various ways.
  

•   CollectSequencingArtifactMetrics (Picard)    Collect metrics to quantify single-base sequencing artifacts.
  

• CollectWgsMetrics (Picard)                   Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.