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=== Qual/Phred (<code>--phred</code> and <code>--qual</code>) ===
=== Qual/Phred (<code>--phred</code> and <code>--qual</code>) ===
Prints a count of the number of times each quality value appears in the file.
Prints a count of the number of times each quality value appears in the file to stderr.
*<code>phred</code> Displays Quality as phred integers [0-93]
*<code>phred</code> Displays Quality as phred integers [0-93]
To only include records that overlap a set of regions, use --regionList and specify a bed file with the regions. If a read overlaps the region, all qualities will be counted even if those bases do not fall in the region. If you only want to count qualities that fall within the region, also specify --withinRegion. Without excluding unmapped reads, it will include soft clips that overlap the region.
To only include records that overlap a set of regions, use --regionList and specify a bed file with the regions. If a read overlaps the region, all qualities will be counted even if those bases do not fall in the region. If you only want to count qualities that fall within the region, also specify --withinRegion. Without excluding unmapped reads, it will include soft clips that overlap the region.
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=== BaseQC (<code>--pBaseQC</code> and <code>--cBaseQC</code> and <code>--baseSum</code>) ===
=== BaseQC (<code>--pBaseQC</code> and <code>--cBaseQC</code> and <code>--baseSum</code>) ===
