The clc_cas_to_sam Program
This tool converts a cas format file to sam or bam format format file.
The clc_cas_to_sam program takes a cas file as input and produces a corresponding SAM file or BAM file. The format generated depends on the filename you choose. If you choose an output file name with the suffix .sam, the output format will be SAM. If you choose an output file name with the suffix .bam, the output format will be BAM.
Please note that the read file(s) that you used in generating the cas file must be present in the same relative location to the cas file as they were when you ran the mapping. This is because, unlike cas format files, SAM and BAM files include all the read data. Thus the read data needs to be present in order to make a valid SAM or BAM file. This also means that the SAM or BAM files created will generally be substantially larger than the cas file they were generated from.
When writing a sam/bam file, each read is given a read mapping quality (MAPQ) score of either 0 or 60. The value 60 is given to reads that mapped uniquely. The value 0 is given to reads that could map equally well to other locations besides the one being reported in the BAM file.
The SAM or BAM file created using the clc_cas_to_sam tool is not sorted or indexed. These steps can be necessary for some types of downstream processing and can be done using the samtools sort program (see http://samtools.sourceforge.net/).
Like cas format files, SAM and BAM files do not contain the reference sequence data.
Further details of the command line options for this tool are provided in Options for All Programs.
Further details about the SAM and BAM formats can be found at http://samtools.sourceforge.net/.