From Genome Analysis Wiki
Jump to navigationJump to search
41 bytes added
, 23:01, 19 April 2019
Line 10: |
Line 10: |
| ==Handling Recalibration/Implementation Notes== | | ==Handling Recalibration/Implementation Notes== |
| | | |
− | Recalibration is a 2-step process that loops through the file twice: | + | Recalibration is a 2-step process that loops through the file twice (stdin is not support as input): |
| # Build Recalibration Table | | # Build Recalibration Table |
| # Apply Recalibration Table | | # Apply Recalibration Table |
Line 59: |
Line 59: |
| | | |
| NOTE: GATK ignores/skips adapters, but our logic does not. | | NOTE: GATK ignores/skips adapters, but our logic does not. |
− |
| |
| | | |
| == How to use it == | | == How to use it == |
Line 136: |
Line 135: |
| | | |
| == Required Generic Parameters == | | == Required Generic Parameters == |
− | {{inBAMInputFile}} | + | {{inBAMInputFile|noStdin=1}} |
| {{outBAMOutputFile}} | | {{outBAMOutputFile}} |
| | | |