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.

       •   Convert the file into SAM format, sort lexicographically by queryname and convert back
           again into BAM format.
           E.g.
           export LC_ALL=C
           samtools view -H file.bam > file_sorted.sam
           samtools view file.bam | sort -k 1 >> file_sorted.sam
           samtools view -bS file_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:
           samtools sort -n -o file_sorted.bam file.bam
           For more information check the man page included in samtools distribution.

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

OPTIONS

   Mandatory options
       -i, --in=in.bam
           input file in BAM format

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

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

       -q f, --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

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

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

       -n, --noIntrons

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

       -s n, --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

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

       -d file, --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

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

       -t n, --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.

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/doc/augustus/README.md.gz.

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