Up: Component summary
Up: Component summary
Function
BamRegrouper
Picard-tools is used to add or replace read group information for each read in the input alignment file. This might be required for files that have faulty information and fail the calling procedure, which heavily uses read group information.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Alignment |
| Authors | Rony Lindell (rony.lindell@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| bam | BAM | Mandatory | Input BAM file. |
Outputs| Name | Type | Description |
|---|---|---|
| alignment | BAM | Final bam file with read groups replaced. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ID | string | "1" | Read group ID. |
| LB | string | (no default) | Read group library. |
| PL | string | (no default) | Read group platform. |
| PU | string | (no default) | Read group platform unit. |
| SM | string | (no default) | Read group sample name. |
| memory | string | "4g" | The amount of java-heap memory being allocated to each GATK and Picard thread, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc. |
| picard | string | "" | Path to Picard directory, e.g. "/opt/picard", which containg the Picard-tools .jar files. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the Picard directory. |
Test cases| Test case | Parameters▼ | IN bam |
OUT alignment |
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|---|---|---|---|---|---|---|
| case1 | properties | bam | (missing) | |||
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# Default run using less memory, |
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