3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→BAM Util Tools
'''File Updates'''
'''File Updates'''
*[[BamUtil: dedup|dedup]] – Mark or remove duplicates, can also perform recalibration
*[[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
*[[BamUtil: recab|recab]] - Recalibrate 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
*[[BamUtil: dumpAsp|dumpAsp]] - 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: dumpAsp|dumpAsp]] - 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: readReference|readReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: readReference|readReference]] - Print the reference string for the specified region to the screen.
=== FASTQ ===
=== FASTQ ===
