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189 bytes added
, 22:14, 4 July 2011
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| # 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] [SEX : 1-MALE, 2-FEMALE] [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. |
| # 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 |
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