Changes

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 ==