3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
**Genotype concordance based detection
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
**Estimate based on population allele frequencies without genotype data
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[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: 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: 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: revert|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
*[[BamUtil: revert|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
*[[BamUtil: squeeze|squeeze]] - Reduce files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
*[[BamUtil: squeeze|squeeze]] - Reduce files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
*[[BamUtil: trimBam| trimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[BamUtil: trimBam| trimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[BamUtil: polishBam|polishBam]] – Add/Update header lines & add RG tag to each record
*[[BamUtil: polishBam|polishBam]] – Add/Update header lines & add RG tag to each record
*[[BamUtil: dumpRefInfo|dumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[BamUtil: dumpRefInfo|dumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[BamUtil: dumpIndex|dumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: dumpIndex|dumpIndex]] - Print the BAM Index to the screen in a readable format
*[[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.
*[[MapabilityScores]] - Definitions of various mappability scores adopted at UCSC genome browser.
*[[MapabilityScores]] - Definitions of various mappability scores adopted at UCSC genome browser.
== Variant Calling ==
== Variant Calling ==
