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, 13:48, 6 November 2012
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| === BAM files === | | === BAM files === |
| + | The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. |
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− | === Index file === | + | FASTQs can be converted to this type of BAM using the [[Mapping Pipeline]]. |
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| + | 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 |
| + | [edit] |
| + | === Index File === |
| + | Each line of the 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] ... |
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| + | Columns: |
| + | # sample id |
| + | # comma separated population labels |
| + | # BAM File 1 |
| + | # BAM File 2 (if applicable) |
| + | :... |
| + | |
| + | : # BAM File N |
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| === Reference Files === | | === Reference Files === |
| + | Reference files are required for doing Variant Calling. |
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| + | See [[#Reference Files| Configuration Files: Reference Files]] for information on how to specify the reference files in the configuration. |
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| === Configuration File === | | === Configuration File === |