Up: Component summary
Up: Component summary
Component
DuplicateMarker
Mark PCR and optical duplicate reads in BAM files using Picard MarkDuplicates. Performed as part of alignment in RNA-seq and DNA whole genome (WGS) or targeted (exome) sequencing analyses.
Complete documentation:
| Version | 2.0 |
|---|---|
| Bundle | sequencing |
| Categories | Alignment |
| Authors | Rony Lindell (amjad.alkodsi@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml duplicateMarker.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | BAM | Mandatory | Input BAM file. The file can be a single-sample or a merged multi-sample alignment file. |
Outputs| Name | Type | Description |
|---|---|---|
| outBam | BAM | Duplicate marked alignment file. |
| outMetrics | TextFile | Duplicate information output file of Picard. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| 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. |
| options | string | "" | Custom Picard parameters can be set in their native format. E.g. "ASSUME_SORTED=true". |
| picard | string | "" | Path to Picard directory, e.g. "/opt/picard", which containg the picard.jar file. If empty string is given (default), PICARD_HOME environment variable is assumed to point to the Picard directory. |
| remove | boolean | false | Remove duplicates instead of only marking them. |
Test cases| Test case | Parameters▼ | IN in |
OUT outBam |
OUT outMetrics |
||
|---|---|---|---|---|---|---|
| case1 | properties | in | (missing) | (missing) | ||
|
memory=1g, |
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