From Genome Analysis Wiki
Jump to navigationJump to search
89 bytes added
, 19:39, 11 January 2013
Line 104: |
Line 104: |
| ==Analyzing a Sample== | | ==Analyzing a Sample== |
| | | |
− | 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 (needed to analyze bam files from targeted/exome sequencing). | + | 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, which can be found in {ROOT_DIR}/test/umake/bams. These contain sequence information for a targeted region in chromosome 20. |
| + | |
| + | In addition to the BAM files, you will need three files to run UMAKE: an index file, a configuration file, and a bed file (needed to analyze BAM files from targeted/exome sequencing). |
| | | |
| | | |