Up: Component summary
Up: Component summary
Component
SubsetBamExtracts reads from a BAM file based on chromosomal regions specified by a user and produces a merged BAM file containing only those regions.
For example, this component can be used to subset a BAM file to contain only those reads which map to genes of interest.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Analysis |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | samtools ; csvkit |
| Source files | component.xml SubsetBam.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | BAM | Mandatory | Input sorted and indexed BAM file. |
| annotation | CSV | Mandatory | DNARegions which are used for subsetting. Locus information can be either in the DNARegion format ('chr:start-end') or as separate columns 'chr,start,end'. Set 'chrCol' parameter accordingly. |
Outputs| Name | Type | Description |
|---|---|---|
| out | BAM | Subsetted BAM file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| chrCol | string | "chr,start,end" | Column name or names for annotation input. If the locus information is on multiple columns, this parameter needs to be a comma-separated list of column names in 'annotation'. Otherwise, the name of the DNARegion formatted column in 'annotation'. |
Test cases| Test case | Parameters▼ | IN in |
IN annotation |
OUT out |
||
|---|---|---|---|---|---|---|
| case1 | properties | (missing) | annotation | (missing) | ||
|
chrCol=chr,start,end |
||||||
| case2 | properties | (missing) | annotation | (missing) | ||
|
chrCol=chr:start-end |
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