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Sample2 fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you prefer, you can create a new index file and change the MERGE_NAME, RGID, SAMPLE, LIBRARY, CENTER, or PLATFORM values. It is recommended that you do not modify existing files in {ROOT_DIR}/test/align.
If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you prefer, you can create a new index file and change the MERGE_NAME, RGID, SAMPLE, LIBRARY, CENTER, or PLATFORM values. It is recommended that you do not modify existing files in {ROOT_DIR}/test/align.
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:
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]].)
===Configuration file===
===Configuration file===
PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20
PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20
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]].)
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]].)
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]].)
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]].)
==Advanced Options==
==Advanced Options==
For further explanation about the other options available in the alignment pipeline, see the [[Mapping_Pipeline|Mapping Pipeline]] page.
For further explanation about advanced options available in the alignment pipeline, see the [[Mapping_Pipeline|Mapping Pipeline]] page.
For further explanation about the other options available in UMAKE, see the [[Variant_Calling_Pipeline_(UMAKE)|Variant Calling Pipeline]] page.
For further explanation about advanced options available in UMAKE, see the [[Variant_Calling_Pipeline_(UMAKE)|Variant Calling Pipeline]] page.
