From Genome Analysis Wiki
Jump to navigationJump to search
58 bytes added
, 17:38, 3 January 2014
Line 47: |
Line 47: |
| </pre> | | </pre> |
| | | |
| + | == Required Parameters == |
| {{inBAMInputFile}} | | {{inBAMInputFile}} |
| | | |
− | == output File <code>(--out)</code>== | + | === output File <code>(--out)</code>=== |
| | | |
| Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. | | Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. |
Line 56: |
Line 57: |
| | | |
| {{RefFile}} | | {{RefFile}} |
| + | |
| + | == Optional Parameters == |
| {{BamIndex}} | | {{BamIndex}} |
| | | |
− | == Region List <code>(--regionList)</code> == | + | === Region List <code>(--regionList)</code> === |
| Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. | | Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. |
| | | |
Line 71: |
Line 74: |
| If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). | | If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). |
| | | |
− | == Gap Size <code>(--gapSize)</code> == | + | === Gap Size <code>(--gapSize)</code> === |
| When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. | | When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. |
| # Write an Empty record indicating no data for that position. | | # Write an Empty record indicating no data for that position. |