Provided by: blasr_5.3+0-2_amd64
samFilter - filter nucleotide sequence alignments in SAM files
samFilter file.sam reference.fasta out.sam [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.
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.
blasr(1) loadPulses(1) pls2fasta(1) samtoh5(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)