Up: Component summary
Up: Component summary
Component
BamCombiner
Merges multiple bam files using the Picard MergeSamFiles. The output bam is a dynamically merged and coordinate sorted bam file.
| Version | 2.0 |
|---|---|
| Bundle | sequencing |
| Categories | Alignment |
| Authors | Amjad Alkodsi (amjad.alkodsi@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml bamCombiner.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | Array<BAM> | Mandatory | Array of bam files. |
Outputs| Name | Type | Description |
|---|---|---|
| out | BAM | The merged alignment bam file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| memory | string | "4g" | The amount of java-heap memory being allocated to PICARD, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc. |
| options | string | "" | Additional MergeSamFiles arguments can be set here. |
| picard | string | "" | Path to picard directory. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the GATK directory. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
|||
|---|---|---|---|---|---|---|
| case1 | properties | in | (missing) | |||
|
memory=1g |
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