xenial (1) samFilter.1.gz

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)