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samtoh5 - convert a SAM file to cmp.h5 format
samtoh5 in.sam reference.fasta out.cmp.h5
- 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.
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1)
samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)