.TH SAMFILTER "1" "July 2015" "samFilter 3ca7fe8" "User Commands"
.SH NAME
samFilter \- filter nucleotide sequence alignments in SAM files
.SH SYNOPSIS
.B samFilter
.I file.sam
.I reference.fasta
.I out.sam
.RI [ options ]
.SH OPTIONS
.TP
.I file.sam
Input SAM file.
.TP
.I reference.fasta
Reference used to generate reads.
.TP
.I out.sam
Output SAM file.
.TP
.BI \-minAlnLength \0value
(50) Report alignments only if their lengths are greater than
\fIvalue\fR.
.TP
.BI \-minAlignLength \0value
Alias of \fB\-minAlnLength\fR
.TP
.BI \-minLength \0value
Alias of \fB\-minAlnLength\fR
.TP
.BI \-minPctSimilarity \0value
.IP
(70) Report alignments only if their percentage similairty is
greater than \fIvalue\0.
.TP
.BI \-minPctIdentity \0value
Alias of \fB\-minPctSimilarity\fR
.TP
.BI \-minPctAccuracy \0value
(70) Report alignments only if their percentage accuray is
greater than \fIvalue\fR.
.TP
.BI \-minAccuracy \0value
Alias of \fB\-minPctAccuracy\fR
.TP
.BI \-hitPolicy \0value
(randombest) Specify a policy to treat multiple hits from [all,
allbest, random, randombest, leftmost]
.RS
.TP
.I all
report all alignments.
.TP
.I allbest
report all equally top scoring alignments.
.TP
.I random
report a random alignment.
.TP
.I randombest
report a random alignment from multiple equally top scoring alignments.
.TP
.I leftmost
report an alignment which has the best alignmentscore and has the smallest
mapping coordinate in any reference.
.RE
.TP
.BI \-scoreSign \0value
(\-1) Whether higher or lower scores are better.
.RS
.TP
\-1
lower is better
.TP
1
higher is better.
.RE
.TP
.BI \-scoreCutoff \0value
(INF) Report alignments only if their scores are no worse than
\fIvalue\fR.
.TP
.BI \-seed \0value
(1) Seed for random number generator.
If seed is 0, then use current time as seed.
.TP
.BI \-holeNumbers \0value
A string of comma-delimited hole number ranges to output hits,
such as '1,2,10-12'. This requires hit titles to be in SMRT read
title format.
.TP
.B \-smrtTitle
Use this option when filtering alignments generated by programs
other than
.BR blasr (1),
e.g. bwa\-sw or gmap. Parse read coordinates
from the SMRT read title. The title is in the format
\fI\,/name/hole/coordinates\/\fP, where coordinates are in the format
\ed+_\ed+, and represent the interval of the read that was
aligned.
.TP
.BI \-titleTable \0value
Use this experimental option when filtering alignments generated
by
.BR blasr (1)
with \fB\-titleTable\fR titleTableName, in which case
reference titles in SAM are represented by their indices (e.g.,
0, 1, 2, ...) in the title table.
.TP
.BI \-filterAdapterOnly \0value
Use this option to remove reads which can only map to adapters
specified in the GFF file.
.TP
.B \-v
Be verbose.
.SH 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
.RB ( blasr (1))
it is defined as the start in the query sequence of the alignment.
When \fB\-smrtTitle\fR 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.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR pls2fasta (1)
.BR samtoh5 (1)
.BR samtom4 (1)
.BR sawriter (1)
.BR sdpMatcher (1)
.BR toAfg (1)