### CollectMultipleMetrics

Takes an input BAM and reference sequence and runs one or more Picard metrics modules at the same time to cut down on I/O. Currently all programs are run with default options and fixed output extesions, but this may become more flexible in future.

Option | Description
--- | ---
INPUT=File | Input SAM or BAM file. Required.
REFERENCE_SEQUENCE=File | Reference sequence fasta Default value: null.
ASSUME_SORTED=Boolean | If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
STOP_AFTER=Integer | Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.
OUTPUT=String | Base name of output files Required.
PROGRAM=Program | Possible values: {CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.