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Revision as of 13:48, 6 November 2012
, 13:48, 6 November 2012no edit summary
=== BAM files ===
=== BAM files ===
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
=== Index file ===
FASTQs can be converted to this type of BAM using the [[Mapping Pipeline]].
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
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=== 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] ...
Columns:
# sample id
# comma separated population labels
# BAM File 1
# BAM File 2 (if applicable)
:...
: # BAM File N
=== Reference Files ===
=== Reference Files ===
Reference files are required for doing Variant Calling.
See [[#Reference Files| Configuration Files: Reference Files]] for information on how to specify the reference files in the configuration.
=== Configuration File ===
=== Configuration File ===
