QTLtools-bamstat1

Usage

Overview

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

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>