Changes

*[[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file.  <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>

*[[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file.  <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>

'''File Updates'''

'''File Updates'''

*[[BamUtil: dedup|dedup]] – Mark or remove duplicates, can also perform recalibration - <span style="color:#D2691E">Coming Soon</span>

*[[BamUtil: dedup|dedup]] – Mark or remove duplicates, can also perform recalibration

*[[BamUtil: recab|recab]] - Recalibrate – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model - <span style="color:#D2691E">Coming Soon</span>

*[[BamUtil: recab|recab]] - Recalibrate – Resource-efficient tool, which recalibrates base qualities based on an adaptive logistic regression model

*[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap

*[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap

*[[BamUtil: filter|filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high

*[[BamUtil: filter|filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high