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.