---
name: "filterBam"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/filterBam"
---

# filterBam(1)

filter BAM file for use with AUGUSTUS tools

## 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.