samtoh5(1) convert a SAM file to cmp.h5 format


samtoh5 in.sam reference.fasta out.cmp.h5 [options]


Input SAM file.
Reference used to generate reads.
Output cmp.h5 file.
Use this option when converting alignments generated from reads produced by the pls2fasta(1) from bas.h5 files by parsing read coordinates from the SMRT read title. The title is in the format ,/name/hole/coordinates/, where coordinates are in the format \d+_\d+, and represent the interval of the read that was aligned.
-readType value
Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
-verbosity value
Set desired verbosity.
Use abbreviated reference names obtained from file.sam instead of using full names from reference.fasta.
Copy all QVs available in the SAM file into the cmp.h5 file. This includes things like InsertionQV and DeletionTag.


Because SAM has optional tags that have different meanings in different programs, careful usage is required in order to have proper output. The "xs" tag in bwa-sw is used to show the suboptimal score, but in PacBio SAM (blasr(1)) it is defined as the start in the query sequence of the alignment. When -smrtTitle is specified, the xs tag is ignored, but when it is not specified, the coordinates given by the xs and xe tags are used to define the interval of a read that is aligned. The CIGAR string is relative to this interval.