FILTERBAM(1)

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. .br E.g. .br export LC_ALL=C .br samtools view -H file.bam > file_sorted.sam .br samtools view file.bam | sort -k 1 >> file_sorted.sam .br samtools view -bS file_sorted.sam > file_sorted.bam .br [be aware: 'export LC_ALL=C' might be used because sort ignores characters like ':'] .br 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: .br samtools sort -n -o file_sorted.bam file.bam .br For more information check the man page included in samtools distribution.

    • bamtools can also sort bam files: .br bamtools sort -byname -in file.bam -out file_sorted.bam .br 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.