Difference between revisions of "BamUtil: mergeBam"
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| − | == | + | = Overview of the <code>rgMergeBam</code> function of <code>bamUtil</code> = |
| + | The <code>rgMergeBam</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs. | ||
rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers. | rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers. | ||
| Line 8: | Line 9: | ||
| − | + | = Usage= | |
<pre> | <pre> | ||
| − | rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile> | + | ./bam rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile> |
| + | </pre> | ||
| + | =Parameters= | ||
| + | <pre> | ||
Required parameters : | Required parameters : | ||
--out/-o : Output BAM file (sorted) | --out/-o : Output BAM file (sorted) | ||
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</pre> | </pre> | ||
| + | [[Category:BamUtil|rgMergeBam]] | ||
| + | [[Category:BAM Software]] | ||
[[Category:Software]] | [[Category:Software]] | ||
| − | |||
| − | |||
Revision as of 14:51, 3 April 2012
Overview of the rgMergeBam function of bamUtil
The rgMergeBam option on the bamUtil executable merges 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
./bam rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>
Parameters
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
