Converting to and from SAM and BAM formats

CLC Assembly Cell includes a tool called clc_cas_to_sam to convert a cas format file to the SAM3.1 or BAM3.2 format. Also included is a tool called clc_sam_to_cas that converts from SAM or BAM format into the cas format.

These tools are described in more detail in their own sections: clc_cas_to_sam and clc_sam_to_cas.


... SAM3.1
Sequence Alignment/Map format
... BAM3.2
BAM is the binary compact format for SAM