QTLtools bamstat - Calculate stats of overlap between an RNAseq BAM file and an
annotation
QTLtools bamstat --bam [sample.bam|sample.sam|sample.cram] --bed
[ gene_annotation.bed] --out output_file
[OPTIONS]
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.
- --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
-
--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
|
- 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
QTLtools(1)
QTLtools website: <
https://qtltools.github.io/qtltools>
Please submit bugs to <
https://github.com/qtltools/qtltools>
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>
Olivier Delaneau (
[email protected]), Halit Ongen
(
[email protected])