Difference between revisions of "BamUtil: mergeBam"
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=== Usage=== | === Usage=== | ||
<pre> | <pre> | ||
| − | rgMergeBam [-v] | + | rgMergeBam [-v]options) --list=<RGAListFile> --out=<outBamFile> |
| + | rgMergeBam [-v] [-L logFile] [-l listFile] [-o outFile] | ||
| − | + | Required parameters : | |
| − | + | --out/-o : Output BAM file (sorted) | |
| − | + | --list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers): | |
| − | + | BAM* : Input BAM file name to be merged | |
| − | + | ID* : Unique read group identifier | |
| − | + | SM* : Sample name | |
| + | LB : Library name | ||
| + | DS : Description | ||
| + | PU : Platform unit | ||
| + | PI : Predicted median insert size | ||
| + | CN : Name of sequencing center producing the read | ||
| + | DT : Date the rn was produced | ||
| + | PL : Platform/technology used to produce the read | ||
| + | * (Required fields) | ||
| + | Optional parameters : | ||
| + | --log/-L : Log file | ||
| + | --verbose/-v : Turn on verbose mode | ||
</pre> | </pre> | ||
Revision as of 18:29, 1 November 2010
RGMergeBAM : Merge multiple BAM files appending ReadGroup IDs
rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.
- Checks that the HD and SQ tags are identical across the BAM files
- Adds @RG headers from a tabular input file containing the fields' info
- Adds RG:Z:[RGID] tag for each record based on the source BAM file
- Ensures that the headers are identical across the input files and that input/output BAM records are sorted
Usage
rgMergeBam [-v]options) --list=<RGAListFile> --out=<outBamFile> rgMergeBam [-v] [-L logFile] [-l listFile] [-o outFile] Required parameters : --out/-o : Output BAM file (sorted) --list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers): BAM* : Input BAM file name to be merged ID* : Unique read group identifier SM* : Sample name LB : Library name DS : Description PU : Platform unit PI : Predicted median insert size CN : Name of sequencing center producing the read DT : Date the rn was produced PL : Platform/technology used to produce the read * (Required fields) Optional parameters : --log/-L : Log file --verbose/-v : Turn on verbose mode
