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)