QTLtools-bamstat

Section: Bioinformatics tools (1)
Updated: 06 May 2020
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NAME

QTLtools bamstat - Calculate stats of overlap between an RNAseq BAM file and an annotation  

SYNOPSIS

QTLtools bamstat --bam [sample.bam|sample.sam|sample.cram] --bed [gene_annotation.bed] --out output_file [OPTIONS]  

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 --filter-mapping-quality.  

OPTIONS

--bed annotation.bed
Annotation of interest REQUIRED.
--bam, -b [in.bam|in.sam|in.cram]
Sequence data in BAM/SAM/CRAM format. REQUIRED.
--out, -o output
Output file name REQUIRED.
--filter-mapping-quality integer
Minimum mapping quality for a read or read pair to be considered. Set this to only include uniquely mapped reads. DEFAULT=10
--filter-keep-duplicates
Keep reads designated as duplicate by the aligner. RECOMMENDED for RNAseq

 

OUTPUT FILE COLUMNS

--out filename
This file does not have header and it contains the following columns:

1     The total number of reads in the BAM file
2     The number of mapped sequencing reads passing the --filter-mapping-quality
3     The number of mapped sequencing reads falling within the annotations specified with --bed
4     The total number of annotations in the --bed file
5     The number of annotations covered by at least one sequencing read

 

EXAMPLES

o Running bamstat on an RNAseq sample mapped with GEM and GENCODE gene annotations:

QTLtools bamstat --bam HG00381.chr22.bam --out HG00381.chr22.bamstat.txt --bed gencode.v19.annotation.bed.gz --filter-mapping-quality 150 --filter-keep-duplicates

 

SEE ALSO

QTLtools(1)  

BUGS

Please submit bugs to <https://github.com/qtltools/qtltools>  

CITATION

Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL discovery and analysis. Nat Commun 8, 15452 (2017). <https://doi.org/10.1038/ncomms15452>  

AUTHORS

Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
OUTPUT FILE COLUMNS
EXAMPLES
SEE ALSO
BUGS
CITATION
AUTHORS

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Time: 14:11:25 GMT, August 24, 2020