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This will create a symbolic link to the test fastq directory from your current directory.
This will create a symbolic link to the test fastq directory from your current directory.
(Click to see more information about: [[Mapping_Pipeline#Sequence_Index_File|the index file]].)
(More information about: [[Mapping_Pipeline#Sequence_Index_File|the index file]].)
===Configuration file===
===Configuration file===
If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line. If you are not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.
If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line. If you are not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.
(Click to see more information about: [[Mapping_Pipeline#Reference_Files|reference files]], [[Mapping_Pipeline#Optional_Configurable_Settings|optional configurable settings]], or [[Mapping_Pipeline#Command-Line_Options|command-line options]].)
(More information about: [[Mapping_Pipeline#Reference_Files|reference files]], [[Mapping_Pipeline#Optional_Configurable_Settings|optional configurable settings]], or [[Mapping_Pipeline#Command-Line_Options|command-line options]].)
ln -s {ROOT_DIR}/test/umake/bams bams
ln -s {ROOT_DIR}/test/umake/bams bams
(Click to see more information about: [[Variant_Calling_Pipeline_(UMAKE)#Index_File|the index file]].)
(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Index_File|the index file]].)
You can copy this to the current directory and use it as-is.
You can copy this to the current directory and use it as-is.
(Click to see more information about: [[Variant_Calling_Pipeline_(UMAKE)#Targeted.2FExome_Sequencing_Settings|targeted/exome sequencing settings]].)
(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Targeted.2FExome_Sequencing_Settings|targeted/exome sequencing settings]].)
where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.
where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.
(Click here for more information about: [[Variant_Calling_Pipeline_(UMAKE)#Configuration_File|the configuration file]], [[Variant_Calling_Pipeline_(UMAKE)#Reference_Files|reference files]].)
(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Configuration_File|the configuration file]], [[Variant_Calling_Pipeline_(UMAKE)#Reference_Files|reference files]].)
