File: filterBam.1.adoc

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# 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.

  - *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. K├Ânig, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.