Changes

==Aligning a Sample==

==Aligning a Sample==

As an example, we can align the sample files used in the automatic test.

As an example, we can align the sample fastq files used in the automatic test. They belong to two different samples, which we will call "Sample1" and "Sample2".  They are found in {ROOT_DIR}/test/align/fastq. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".)

To make this easier, change to the {ROOT_DIR}/test/align directory. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) It contains an index file and a configuration file that can be used directly.

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

  make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log &

  make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log &

The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.

The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory.  If you see two BAM files, one for each sample, then you have successfully aligned the fastq files.

==Analyzing a Sample==

==Analyzing a Sample==

Using UMAKE, you can analyze the BAM files generated in the previous step and generate a VCF file.  Once again, we can analyze BAM files used in the automatic test.  You will need three files for this: index, configuration, and bed.

Using UMAKE, you can analyze BAM files by calling SNPs, and generate a VCF file containing the results.  Once again, we can analyze BAM files used in the automatic test.  For this example, we have 60 BAM files, found in {ROOT_DIR}/test/umake/bams.  In addition to the BAM files, you will need three files to run UMAKE: an index file, a configuration file, and a bed file.

===Running UMAKE===

===Running UMAKE===

If you added an OUTDIR line to the configuration file, you can run UMAKE with the following command:

If you added an OUT_DIR line to the configuration file, you can run UMAKE with the following command:

  {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2

  {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2

If you have not added an OUTDIR line to the configuration file, you can specify the output directory directly with the following command:

If you have not added an OUT_DIR line to the configuration file, you can specify the output directory directly with the following command:

  {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --outdir {OUT_DIR} --snpcall --numjobs 2

  {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --outdir {OUT_DIR} --snpcall --numjobs 2

where {OUT_DIR} is the directory in which you want the output to be stored.

where {OUT_DIR} is the directory in which you want the output to be stored.

Either command will perform SNP calling on the test samples. The resulting VCF files from this will be located in {OUT_DIR}/vcfs/chr20.

Either command will perform SNP calling on the test samples. If you find the resulting VCF files located in {OUT_DIR}/vcfs/chr20, then you have successfully called the SNPs from the test BAM files.