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| ==Aligning a Sample== | | ==Aligning a Sample== |
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− | 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}".) |
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− | 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. |
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| 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 & |
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− | 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. |
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| ==Analyzing a Sample== | | ==Analyzing a Sample== |
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− | 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. |
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| ===Running UMAKE=== | | ===Running UMAKE=== |
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− | 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: |
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| {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2 | | {ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2 |
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− | 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: |
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| {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 |
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| 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. |
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− | 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. |
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