Changes

To make this easier, change to the test/align directory.  It contains an index file and a configuration file that can be used directly.

To make this easier, change to the test/align directory.  It contains an index file and a configuration file that can be used directly.

===3.1 Index file===

===3.1 Index file===

There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format.  Normally, we would need to build an index file for these files. Conveniently, an index file has already been created for the automatic test samples in indexFile.txt. It contains the following information in tab-delimted format:

There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format.  Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It contains the following information in tab-delimted format:

  MERGE_NAME FASTQ1                          FASTQ2                          RGID  SAMPLE    LIBRARY CENTER PLATFORM

  MERGE_NAME FASTQ1                          FASTQ2                          RGID  SAMPLE    LIBRARY CENTER PLATFORM

If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct.

If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct.

===3.2 Configuration file===

 

AS = NCBI37

FA_REF = $(REF_DIR)/human_g1k_v37_chr20.fa

DBSNP_VCF = $(REF_DIR)/dbsnp.b130.ncbi37.chr20.vcf.gz

PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20

 

If you are in the 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.