Up: Component summary
Up: Component summary
Function
BamReorderThis function reorders reads in a BAM file to match the contig ordering in the provided reference file.
| 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 |
|---|---|---|---|
| reference | FASTA | Mandatory | The reference fasta file. |
| bam | BAM | Mandatory | Input BAM file. |
Outputs| Name | Type | Description |
|---|---|---|
| alignment | BAM | Final reordered bam file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| incomplete | boolean | false | Allow an incomplete overlap of input bam file contigs with the reference contigs. |
| 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 reference |
IN bam |
OUT alignment |
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|---|---|---|---|---|---|---|
| case1 | properties | reference | bam | (missing) | ||
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# Default run using less memory, |
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