QTLtools-bamstat(1)

💖 QTLtools-bamstat(1) 💖

Okay bestie, this is the manual page for QTLtools-bamstat(1), filed under the Bioinformatics tools section 🧚 Let's get into it!

✨ NAME ✨

So the name is QTLtools bamstat, and it's giving stats of overlap 📊 It calculates stats of overlap between an RNAseq BAM file and an annotation. Iconic. 💅

🎀 SYNOPSIS 🎀

Here's the vibe for how you call it 💜

QTLtools bamstat --bam [sample.bam|sample.sam|sample.cram] --bed
[gene_annotation.bed]  --out output_file [OPTIONS]

🌸 DESCRIPTION 🌸

This mode is the counting queen 👑 It counts how many RNAseq reads you've got, and how many of them overlap with your annotation file. ngl, we recommend using uniquely mapping reads only, and you do that by picking the right --filter-mapping-quality 🦋

---

✨ OPTIONS ✨

Okay, the options are where it gets spicy 🌶️

• --bed annotation.bed — The annotation of interest. REQUIRED 🧬
• --bam, -b [in.bam|in.sam|in.cram] — Your sequence data, in BAM, SAM, or CRAM format. REQUIRED 💖
• --out, -o output — The output file name. REQUIRED 📝
• --filter-mapping-quality integer — The minimum mapping quality a read or read pair needs before it gets considered. Set this to only include uniquely mapped reads. DEFAULT=10 ✨
• --filter-keep-duplicates — Keeps the reads the aligner marked as duplicates. RECOMMENDED for RNAseq 🔥

---

🦋 OUTPUT FILE COLUMNS 🦋

Real talk, this one's a little plain, but it matters. The --out filename file does not have a header 🙈 It has these five columns, in this order:

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 🧚

• 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 🌈

Check out QTLtools(1) for the full picture 👑

QTLtools website: <https://qtltools.github.io/qtltools> 💜

🐞 BUGS 🐞

Found something broken? 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) 🌸

---

Source: QTLtools-v1.3, last updated 06 May 2020, manual page QTLtools-bamstat(1). Bye bestie, go count some reads! 🦋✨💖