NAME
samFilter - 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.
SEE ALSO
blasr(1) loadPulses(1) pls2fasta(1) samtoh5(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)