Changes

==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).