This is the command samtoh5 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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