NAME

       samtoh5 - convert a SAM file to cmp.h5 format

SYNOPSIS

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

OPTIONS

       in.sam Input SAM file.

       reference.fasta
              Reference used to generate reads.

       out.cmp.h5
              Output cmp.h5 file.

       -smrtTitle
              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.

       -useShortRefName
              Use  abbreviated  reference  names  obtained  from  file.sam  instead  of  using  full  names from
              reference.fasta.

       -copyQVs
              Copy all QVs available in  the  SAM  file  into  the  cmp.h5  file.   This  includes  things  like
              InsertionQV and DeletionTag.

NOTES

       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.

SEE ALSO

       blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)

samtoh5 3ca7fe8                                     July 2015                                         SAMTOH5(1)