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.