Up: Component summary
Up: Component summary
Function
RNAVariantCallerVariant calling in RNAseq data using HaplotypeCaller and VariantFiltration in GATK. The function with default values follows the GATK best practices as seen on 12.09.2016
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Analysis |
| Authors | Amjad Alkodsi (amjad.alkodsi@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. |
| in | BAM | Mandatory | Input BAM file. |
Outputs| Name | Type | Description |
|---|---|---|
| out | VCF | Filtered Variant calls |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| callEmit | string | "20.0,20.0" | Comma-separated values of stand_call_conf and stand_emit_conf parameters respectively. |
| cluster | string | "3" | Minimum number of variants in a defined window to consider them clustered. |
| filterNames | string | "FS,QD" | Comma-separated names of filters to be applied. For example use "FS,QD" for two filters. |
| filteringOptions | string | "" | Other options to be passed to VariantFiltration. |
| filters | string | "FS > 30.0,QD < 2.0" | Comma-separated filters to be applied. The length and order should match the one in filterNames. |
| gatkPath | string | "" | Path to GATK directory containing the 'GenomeAnalysisTK.jar'. If empty string is given (default), GATK_HOME environment variable is assumed to point to the GATK directory where GenomeAnalysisTK.jar is located. |
| haplotypeOptions | string | "" | Other options to pass to HaplotypeCaller |
| 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. |
| window | string | "35" | Window size in bp for clustered variants filtering. Set to 0 to deactivate. |
Test cases| Test case | Parameters▼ | IN reference |
IN in |
OUT out |
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|---|---|---|---|---|---|---|
| case1 | properties | reference | in | (missing) | ||
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memory=2g |
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