QTLtools-bamstat(1)

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)

QTLtools website: <https://qtltools.github.io/qtltools>

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)