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.\" Manpage for QTLtools bamstat.
.\" Contact halitongen@gmail.com to correct errors or typos.
.TH QTLtools-bamstat 1 "06 May 2020" "QTLtools-v1.3" "Bioinformatics tools"
.SH NAME
QTLtools bamstat \- Calculate stats of overlap between an RNAseq BAM file and an annotation
.SH SYNOPSIS
.B QTLtools bamstat \-\-bam [\fIsample.bam|sample.sam|sample.cram\fB] \-\-bed [\fIgene_annotation.bed\fB] \fB \-\-out \fIoutput_file
[\fB\fIOPTIONS\fR]
.SH DESCRIPTION
This mode counts the number of RNAseq reads, and the ones that overlap with an annotation file.
We recommend using uniquely mapping reads only by specifying the correct \fB\-\-filter\-mapping\-quality\fR.
.SH OPTIONS
.TP
.B \-\-bed \fI annotation.bed\fB
Annotation of interest
REQUIRED.
.TP
.B \-\-bam, \-b [\fIin.bam\fR|\fIin.sam\fR|\fIin.cram\fB]
Sequence data in BAM/SAM/CRAM format.
REQUIRED.
.TP
.B \-\-out, \-o \fIoutput\fR
Output file name
REQUIRED.
.TP
.B \-\-filter\-mapping\-quality \fIinteger\fR
Minimum mapping quality for a read or read pair to be considered.
Set this to only include uniquely mapped reads.
DEFAULT=10
.TP
.B \-\-filter\-keep\-duplicates
Keep reads designated as duplicate by the aligner.
RECOMMENDED for RNAseq
.SH OUTPUT FILE COLUMNS
.TP 1
.BI \-\-out " filename
This file does not have header and it contains the following columns:
.TS
n lx .
1 T{
The total number of reads in the BAM file
T}
2 T{
The number of mapped sequencing reads passing the \fB\-\-filter\-mapping\-quality\fR
T}
3 T{
The number of mapped sequencing reads falling within the annotations specified with \fB\-\-bed\fR
T}
4 T{
The total number of annotations in the \fB\-\-bed\fR file
T}
5 T{
The number of annotations covered by at least one sequencing read
T}
.TE
.SH EXAMPLES
.IP o 2
Running bamstat on an RNAseq sample mapped with GEM and GENCODE gene annotations:
.IP "" 2
QTLtools bamstat \-\-bam HG00381.chr22.bam \-\-out HG00381.chr22.bamstat.txt \-\-bed gencode.v19.annotation.bed.gz \-\-filter\-mapping\-quality 150 \-\-filter\-keep\-duplicates
.SH SEE ALSO
.IR QTLtools (1)
.\".IR QTLtools-bamstat (1),
.\".IR QTLtools-mbv (1),
.\".IR QTLtools-pca (1),
.\".IR QTLtools-correct (1),
.\".IR QTLtools-cis (1),
.\".IR QTLtools-trans (1),
.\".IR QTLtools-fenrich (1),
.\".IR QTLtools-fdensity (1),
.\".IR QTLtools-rtc (1),
.\".IR QTLtools-rtc-union (1),
.\".IR QTLtools-extract (1),
.\".IR QTLtools-quan (1),
.\".IR QTLtools-rep (1),
.\".IR QTLtools-gwas (1),
.PP
QTLtools website: <https://qtltools.github.io/qtltools>
.SH BUGS
Please submit bugs to <https://github.com/qtltools/qtltools>
.SH
CITATION
Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL discovery and analysis. \fINat Commun\fR \fB8\fR, 15452 (2017).
<https://doi.org/10.1038/ncomms15452>
.SH AUTHORS
Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)
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