NAME

       filterbam - filter BAM file for use with AUGUSTUS tools

SYNOPSIS

       filterBam --in in.bam --out out.bam [options]

DESCRIPTION

       The input file must be sorted lexicographically by 'queryname', with e.g.

       •   sort -k 1,1 [be aware: 'export LC_ALL=C' might be used  because sort ignores characters like ':']
           Also, please bear in mind that this will require converting your BAM file into SAM.

       •   samtools and bamtools provide facilities to do the sorting, but they are not guaranteed to work
           because of the problem mentioned above.

       •   In the case of samtools, the command is: 'samtools sort [-n] file.bam'. The option [-n] should sort
           by query name, just as 'sort -k 10,10' would do in a PSL file. Without options, the sorting will be
           done by reference name and target coordinate, just as a  'sort -n -k 16,16 | sort -k 14,14' would do
           with PSL. For more information check the man page included in samtools distribution.

       •   bamtools can also sort bam files: bamtools sort -queryname -in file.bam, but only provides the option
           to do it by queryname.

       If the option 'paired' is used, then alignment names must include suffixes /1,/2 or /f,/r.

OPTIONS

       --best
           output all best matches that satisfy minId and minCover (default 0)

       --noIntrons
           do not allow longer gaps -for RNA-RNA alignments- (default 0)

       --paired
           require that paired reads are on opposite strands of same target (default 0). NOTE: see prerequisite
           section above.

       --uniq
           take only best match, iff, second best is much worse  (default 0)

       --verbose
           output debugging info (default 0)

       --insertLimit n
           maximum assumed size of inserts (default 10)

       --maxIntronLen n
           maximal separation of paired reads (default 500000)

       --maxSortesTest n
           maximal sortedness (default 100000)

       --minCover n
           minimal percentage of coverage of the query read (default 80)

       --minId n
           minimal percentage of identity (default 92)

       --minIntronLen n
           minimal intron length  (default 35)

       --uniqThresh n
           threshold % for uniq, second best must be at most this fraction of best (default 0.96)

       --commonGeneFile s
           file name in which to write cases where one read maps several different genes

       --pairBedFile s
           file name of pairedness coverage: a BED format file in which for each position the number of filtered
           read pairs is reported that contain the position in or between the reads

       --pairwiseAlignments
           use in case alignments were done in pairwise fashion (default:  0)

AUTHORS

       AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

ADDITIONAL DOCUMENTATION

       An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.

                                                                                                    FILTERBAM(1)