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Tutorial: GotCloud

441 bytes added, 01:44, 10 January 2013
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==Aligning a Sample==
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.
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. If you see two BAM files, one for each sample, then you have successfully aligned the fastq files.
==Analyzing a Sample==
Using UMAKE, you can analyze the BAM files generated in the previous step by calling SNPs, and generate a VCF filecontaining the results. Once again, we can analyze BAM files used in the automatic test. You 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 for thisto run UMAKE: an indexfile, a configurationfile, and a bedfile.
===Running UMAKE===
If you added an OUTDIR 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
If you have not added an OUTDIR 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
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 If you find the resulting VCF files from this will be located in {OUT_DIR}/vcfs/chr20, then you have successfully called the SNPs from the test BAM files.
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