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