The input BAM file must be sorted by target (=genome) sequence
names and within the sequences by begin coordinates.
Parameters:¶
--in=example.bam
Input BAM file. This option can be omitted only on UNIX
platforms. Then bam2hints reads from the standard input stream.
--out=hints.gff
Output hints gff file. If this option is omitted, then
bam2hints will write to the standard output stream.
--priority=n/-p
priority of hint group (set to 4)
--maxgaplen=n/-g
gaps at most this length are simply closed (set to
14)
--minintronlen=n/-m
alignments with gaps shorter than this and longer than
maxgaplen are discarded (set to 32)
--maxintronlen=n/-M
alignments with longer gaps are discarded (set to
350000)
--MinEndBlockLen=n/-b
minimum length of a 'dangling' exon (set to 8)
--maxQgaplen=n/-q
maximum length of gap in query (cDNA) sequence (set to
5)
--exonhints/-x
compute exonpart, exon and splice site hints in addition
to intron hints (set to 0=Off). You should generate exonpart hints from
RNA-Seq using wiggle (.wig) input to wig2hints.
--ep_cutoff=n/-e
this many bp are cut off of each exonpart hint at end of
alignment (set to 10)
--source=s/-s
source identifier (set to 'E')
--intronsonly/-I
only retrieve intron hints (e.g. because the exon(part)
hints are retrieved by converting to a wig track, set to 1=On). Deprecated as
this is the default now.
--nomult/-n
do not summarize multiple identical intron hints to a
single one (set to 0=Off)
--remove_redundant/-r
only keep the strongest hint for a region (set to
0=Off)
--maxcoverage=n/-C
maximal number of hints at a given position (0: filtering
deactivated). A high value causes long running time of AUGUSTUS in regions
with thousands of cDNA alignments. (set to 0)
--ssOn/-S
include splice site (dss, ass) hints in output (set to
0=Off)
--trunkSS/-T
include splice sites hints from the ends of a truncated
alignment (contig too short, set to 0=Off)
--score=f/-s
fill this number in in the score column (set to 0)
--maxgenelen=n/-G
alignments of the same clone are considered to be of the
same gene if not separated by more than this (set to 400000). Alignments that
span more than this are ignored, but better filter long introns through an
alignment program.
