Man page - qtltools-bamstat(1)

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Manual

QTLtools-bamstat

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

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:

Image grohtml-977990-1.png

EXAMPLES

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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)