table of contents
QTLtools-bamstat(1) | Bioinformatics tools | 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 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)
06 May 2020 | QTLtools-v1.3 |