File: filterBam.1

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'\" t
.\"     Title: filterbam
.\"    Author: [see the "AUTHORS" section]
.\" Generator: Asciidoctor 1.5.5.dev
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "FILTERBAM" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\\$2 \(laURL: \\$1 \(ra\\$3
..
.if \n[.g] .mso www.tmac
.LINKSTYLE blue R < >
.SH "NAME"
filterbam \- filter BAM file for use with AUGUSTUS tools
.SH "SYNOPSIS"
.sp
\fBfilterBam\fP \-\-in in.bam \-\-out out.bam [options]
.SH "DESCRIPTION"
.sp
The input file must be sorted lexicographically by \(aqqueryname\(aq, with e.g.
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fBsort \-k 1,1\fP [be aware: \(aqexport LC_ALL=C\(aq might be used  because sort ignores characters like \(aq:\(aq]
Also, please bear in mind that this will require converting your BAM file into SAM.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fBsamtools\fP and \fBbamtools\fP provide facilities to do the sorting,
but they are not guaranteed to work because of the problem mentioned above.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
In the case of \fBsamtools\fP, the command is: \(aqsamtools sort [\-n] file.bam\(aq.
The option [\-n] should sort by query name, just as \(aqsort \-k 10,10\(aq would do in a PSL file.
Without options, the sorting will be done by reference name and target coordinate, just as a  \(aqsort \-n \-k 16,16 | sort \-k 14,14\(aq would do with PSL.
For more information check the man page included in samtools distribution.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
bamtools can also sort bam files: \fBbamtools sort \-queryname \-in file.bam\fP,
but only provides the option to do it by queryname.
.RE
.sp
If the option \(aqpaired\(aq is used, then alignment names must include suffixes /1,/2 or /f,/r.
.SH "OPTIONS"
.sp
\fB\-\-best\fP
.RS 4
output all best matches that satisfy minId and minCover (default 0)
.RE
.sp
\fB\-\-noIntrons\fP
.RS 4
do not allow longer gaps \-for RNA\-RNA alignments\- (default 0)
.RE
.sp
\fB\-\-paired\fP
.RS 4
require that paired reads are on opposite strands of same target
(default 0). NOTE: see prerequisite section above.
.RE
.sp
\fB\-\-uniq\fP
.RS 4
take only best match, iff, second best is much worse  (default 0)
.RE
.sp
\fB\-\-verbose\fP
.RS 4
output debugging info (default 0)
.RE
.sp
\fB\-\-insertLimit n\fP
.RS 4
maximum assumed size of inserts (default 10)
.RE
.sp
\fB\-\-maxIntronLen n\fP
.RS 4
maximal separation of paired reads (default 500000)
.RE
.sp
\fB\-\-maxSortesTest n\fP
.RS 4
maximal sortedness (default 100000)
.RE
.sp
\fB\-\-minCover n\fP
.RS 4
minimal percentage of coverage of the query read (default 80)
.RE
.sp
\fB\-\-minId n\fP
.RS 4
minimal percentage of identity (default 92)
.RE
.sp
\fB\-\-minIntronLen n\fP
.RS 4
minimal intron length  (default 35)
.RE
.sp
\fB\-\-uniqThresh n\fP
.RS 4
threshold % for uniq, second best must be at most this fraction of best (default 0.96)
.RE
.sp
\fB\-\-commonGeneFile s\fP
.RS 4
file name in which to write cases where one read maps several different genes
.RE
.sp
\fB\-\-pairBedFile s\fP
.RS 4
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
.RE
.sp
\fB\-\-pairwiseAlignments\fP
.RS 4
use in case alignments were done in pairwise fashion (default:  0)
.RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. K├Ânig, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
.sp
An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.