java -jar picard.jar

Reference

Prints a SAM or BAM file to the screen.

Category

Sam/Bam Manipulation

Usage

java -jar picard.jar ViewSam

Manual

INPUT (String)    The SAM or BAM file or GA4GH url to view. Required.
ALIGNMENT_STATUS (AlignmentStatus)    Print out all reads, just the aligned reads or just the unaligned reads. Default value: All. This option can be set to 'null' to clear the default value. Possible values: {Aligned, Unaligned, All}
PF_STATUS (PfStatus)    Print out all reads, just the PF reads or just the non-PF reads. Default value: All. This option can be set to 'null' to clear the default value. Possible values: {PF, NonPF, All}
HEADER_ONLY (Boolean)    Print the SAM header only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
RECORDS_ONLY (Boolean)    Print the alignment records only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INTERVAL_LIST (File)    An intervals file used to restrict what records are output. Default value: null.

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