filterBam1
Filter bam file for use with augustus tools
Usage
filterBam --in
in.bam
--out
out.bam
[options]
Overview
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.
Additional documentation
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.
--help since Debian 12 (Bookworm);
--in since Debian 12 (Bookworm);
--out since Debian 12 (Bookworm);
--threads since Debian 12 (Bookworm);
-b since Debian 12 (Bookworm);
-c since Debian 12 (Bookworm);
-d since Debian 12 (Bookworm);
-e since Debian 12 (Bookworm);
-g since Debian 12 (Bookworm);
-h since Debian 12 (Bookworm);
-i since Debian 12 (Bookworm);
-l since Debian 12 (Bookworm);
-n since Debian 12 (Bookworm);
-o since Debian 12 (Bookworm);
-p since Debian 12 (Bookworm);
-q since Debian 12 (Bookworm);
-s since Debian 12 (Bookworm);
-t since Debian 12 (Bookworm);
-u since Debian 12 (Bookworm);
-v since Debian 12 (Bookworm);
-w since Debian 12 (Bookworm);
-x since Debian 12 (Bookworm).
--minIntronLen until Debian 11 (Bullseye).