From Genome Analysis Wiki
Jump to navigationJump to search
359 bytes added
, 18:29, 1 November 2010
Line 10: |
Line 10: |
| === Usage=== | | === Usage=== |
| <pre> | | <pre> |
− | rgMergeBam [-v] [-l listFile] [-o outFile] [-L logFile] [inputBAMfile1] [inputBAMfile2] ... | + | rgMergeBam [-v]options) --list=<RGAListFile> --out=<outBamFile> |
| + | rgMergeBam [-v] [-L logFile] [-l listFile] [-o outFile] |
| | | |
− | Required arguments:
| + | Required parameters : |
− | -l listFile : File containing RG tags including [BAM] [ID] [SM] [LB]
| + | --out/-o : Output BAM file (sorted) |
− | -o outFile : output BAM file name
| + | --list/-l : RGAList File. Tab-delimited list consisting of following columns (with headers): |
− | Optional arguments:
| + | BAM* : Input BAM file name to be merged |
− | -L logFile : log file name. default is listFile.log
| + | ID* : Unique read group identifier |
− | -v : turn on verbose mode
| + | 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> |