samFilter(1)
filter nucleotide sequence alignments in SAM files
SYNOPSIS
samFilter
file.sam
reference.fasta
out.sam
[options]
OPTIONS
- file.sam
-
Input SAM file.
- reference.fasta
-
Reference used to generate reads.
- out.sam
-
Output SAM file.
- -minAlnLength value
-
(50) Report alignments only if their lengths are greater than
value.
- -minAlignLength value
-
Alias of -minAlnLength
- -minLength value
-
Alias of -minAlnLength
- -minPctSimilarity value
-
-
(70) Report alignments only if their percentage similairty is
greater than value .
-minPctIdentity value
-
Alias of -minPctSimilarity
- -minPctAccuracy value
-
(70) Report alignments only if their percentage accuray is
greater than value.
- -minAccuracy value
-
Alias of -minPctAccuracy
- -hitPolicy value
-
(randombest) Specify a policy to treat multiple hits from [all,
allbest, random, randombest, leftmost]
-
- all
-
report all alignments.
- allbest
-
report all equally top scoring alignments.
- random
-
report a random alignment.
- randombest
-
report a random alignment from multiple equally top scoring alignments.
- leftmost
-
report an alignment which has the best alignmentscore and has the smallest
mapping coordinate in any reference.
- -scoreSign value
-
(-1) Whether higher or lower scores are better.
-
- -1
-
lower is better
- 1
-
higher is better.
- -scoreCutoff value
-
(INF) Report alignments only if their scores are no worse than
value.
- -seed value
-
(1) Seed for random number generator.
If seed is 0, then use current time as seed.
- -holeNumbers value
-
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.
- -smrtTitle
-
Use this option when filtering alignments generated by programs
other than
blasr(1),
e.g. bwa-sw or gmap. Parse 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.
- -titleTable value
-
Use this experimental option when filtering alignments generated
by
blasr(1)
with -titleTable titleTableName, in which case
reference titles in SAM are represented by their indices (e.g.,
0, 1, 2, ...) in the title table.
- -filterAdapterOnly value
-
Use this option to remove reads which can only map to adapters
specified in the GFF file.
- -v
-
Be verbose.
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.