samFilter(1) filter nucleotide sequence alignments in SAM files


samFilter file.sam reference.fasta out.sam [options]


Input SAM file.
Reference used to generate reads.
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]
report all alignments.
report all equally top scoring alignments.
report a random alignment.
report a random alignment from multiple equally top scoring alignments.
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.
lower is better
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.
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.
Be verbose.


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.