From Genome Analysis Wiki
Jump to navigationJump to search
No change in size
, 08:29, 6 July 2011
Line 56: |
Line 56: |
| UMAKE requires three types of input files (1) a set of BAM files (2) index file (3) configuration file | | UMAKE requires three types of input files (1) a set of BAM files (2) index file (3) configuration file |
| | | |
− | # BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
| + | * BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. |
− | # Each line of Index file represents each individual under the following format. Note that multiple BAMs per individual may be provided.
| + | * Each line of Index file represents each individual under the following format. Note that multiple BAMs per individual may be provided. |
| [SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ... | | [SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ... |
− | # Additional input Files including Pedigree files (PED format) (to specify gender information in chrX calling), Target information (UCSC's BED format) in targeted or whole exome capture sequencing may be provided.
| + | * Additional input Files including Pedigree files (PED format) (to specify gender information in chrX calling), Target information (UCSC's BED format) in targeted or whole exome capture sequencing may be provided. |
− | # Configuration file contains core information of run-time options including the software binaries and command line arguments. Refer to the example configuration file for further information
| + | * Configuration file contains core information of run-time options including the software binaries and command line arguments. Refer to the example configuration file for further information |
| | | |
| == Software Components == | | == Software Components == |