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= Overview of the <code>rgMergeBam</code> function of <code>bamUtil</code> =
= Overview of the <code>mergeBam</code> function of <code>bamUtil</code> =
The <code>rgMergeBam</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs.
The <code>mergeBam</code> option on the [[bamUtil]] executable merges multiple BAM files appending ReadGroup IDs if necessary.
rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.
As of version 1.0.7, this program was renamed from rgMergeBam to mergeBam.
* 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
mergeBam merges multiple sorted SAM/BAM files into one BAM file like 'samtools merge' command, but merges BAM headers.
* Adds RG:Z:[RGID] tag for each record based on the source BAM file
* Checks that the non RG header fields are identical across the BAM files
* Ensures that the headers are identical across the input files and that input/output BAM records are sorted
* Checks that the input SAM/BAM records are sorted
* If --list option is used:
** Ensures that the headers are identical across the input 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
* If --in is used:
** Merges the RG headers from the files, checking that they RG IDs are unique or if they are the same that the rest of the fields are the same
= Usage=
= Usage=
<pre>
<pre>
./bam rgMergeBam [-v] [--log logFile] --list <listFile> --out <outFile>
./bam mergeBam [-v] [--log logFile] [--list <listFile>|--in <inputFile> --in <inputFile>] --out <outFile>
</pre>
</pre>
Required parameters :
Required parameters :
--out/-o : Output BAM file (sorted)
--out/-o : Output BAM file (sorted)
--in/-i : BAM file to be input, must be more than one of these options.
cannot be used with --list/-l
--list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers):
--list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers):
BAM* : Input BAM file name to be merged
BAM* : Input BAM file name to be merged
</pre>
</pre>
[[Category:BamUtil|rgMergeBam]]
[[Category:BamUtil|mergeBam]]
[[Category:BAM Software]]
[[Category:BAM Software]]
[[Category:Software]]
[[Category:Software]]
