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filterBam - filter BAM file for use with AUGUSTUS tools


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


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.



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


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


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


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


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


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


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


An exhaustive documentation can be found in the file /usr/share/doc/augustus/