Up: Component summary
Up: Component summary
Function
BamReducer
This function reduces the reads in a bam file using the Genome Analysis Toolkit (GATK) 2 and outputs a dramatically more compressed bam file. The output file is callable for variants (at least using GATK) and also visualizable. Note that GATK 1 does not include this functionality.
Complete documentation:
| 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 | Reduced alignment bam file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| cleanup | boolean | false | Removes input alignment files by replacing them with empty files. Use this to save space when the previous alignments are no longer needed. |
| downsample | int | -1 | The coverage of a variable region is downsampled to size INT. Use -1 if you want to use the default downsampling value of GATK. A value of 0 turns downsampling off. If memory problems occur, reducing the value e.g. down to 40 might help. |
| gatk | string | "" | Path to GATK directory containing the 'GenomeAnalysisTK.jar' file. If empty string is given (default), GATK_HOME environment variable is assumed to point to the GATK directory where GenomeAnalysisTK.jar is located. |
| memory | string | "4g" | The amount of java-heap memory being allocated to the GATK thread, given in the format "4g" for 4 gigabytes or "2560m" for 2560 megabytes (2,5g) etc. |
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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