filterBam - filter BAM file for use with AUGUSTUS tools

       An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.

                                                                                                    FILTERBAM(1)

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

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

       •   Convert the file into SAM format, sort lexicographically by queryname and convert back again into BAM
           format.
           E.g.
           exportLC_ALL=Csamtoolsview-Hfile.bam>file_sorted.samsamtoolsviewfile.bam|sort-k1>>file_sorted.samsamtoolsview-bSfile_sorted.sam>file_sorted.bam
           [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 to sort by 'queryname' is:
           samtoolssort-n-ofile_sorted.bamfile.bam
           For more information check the man page included in samtools distribution.

       •   bamtools can also sort bam files:
           bamtoolssort-byname-infile.bam-outfile_sorted.bam
           but only provides the option to do it by queryname.

       filterBam - filter BAM file for use with AUGUSTUS tools

Mandatoryoptions-i, --in=in.bam
           input file in BAM format

       -o, --out=out.bam
           output file in BAM format

   Optionaloptions-u, --uniq
           keep only the best match, remove all matches, if the second best is not much worse

       -qf, --uniqThresh=f
           threshold % for uniq, second best must be lower than this fraction of best to keep the best match
           (default 0.96)

       -b, --best
           output all best matches that satisfy minId and minCover

       -en, --minId=n
           minimal percentage of identity (default 92)

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

       -n, --noIntrons

           do not allow longer gaps -for RNA-RNA alignments-
       -ln, --insertLimit=n
           maximum assumed size of inserts (default 10)

       -sn, --maxSortesTest=n
           test if input file is sorted by query name for this number of alignments (default 100000)

       -p, --paired
           require that paired reads are on opposite strands of same target. Requires alignment names to contain
           the suffixes /1,/2 or /f,/r.

       -w, --pairwiseAlignments
           use in case alignments were done in pairwise fashion

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

       -dfile, --pairBedFile=file
           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

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

       -tn, --threads=n
           use n threads for compression/decompression (default 1); available only if library SeqLib >= 1.2 is
           used

       -v, --verbose
           output debugging info

       -h, --help
           produce help message.

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