table of contents
| FILTERBAM(1) | 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.
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.
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.
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.
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.