From Genome Analysis Wiki
Jump to navigationJump to search
23 bytes added
, 11:02, 9 March 2015
Line 15: |
Line 15: |
| * [[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 file 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 file 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 the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!' | + | * [[BamUtil: trimBam|trimBam]] - Trim the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!' or by doing soft clips |
| * [[BamUtil: mergeBam|mergeBam]] - Merge multiple BAMs and headers appending ReadGroupIDs if necessary | | * [[BamUtil: mergeBam|mergeBam]] - Merge multiple BAMs and headers appending ReadGroupIDs if necessary |
| * [[BamUtil: polishBam|polishBam]] - Add/update header lines & add the RG tag to each record | | * [[BamUtil: polishBam|polishBam]] - Add/update header lines & add the RG tag to each record |