QTLtools-extract(1)

🌸 Hey bestie, it's QTLtools extract 🌸

Lowkey this one lives in the Bioinformatics tools squad 🧬

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✨ NAME ✨

Okay so QTLtools extract is the Data extraction mode 💅 That's literally its whole personality.

🦋 SYNOPSIS 🦋

Here's how you call it, no cap 👀

QTLtools extract [--vcf --bed --cov] relevant_file --out output_prefix
[OPTIONS]

💜 DESCRIPTION 💜

This mode grabs all the data from your files and squishes it into one flat file 🥞 It also imputes all the missing data, so no gaps, no cap ✨

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👑 OPTIONS 👑

• --vcf [in.vcf|in.bcf|in.vcf.gz] — Your genotypes, in VCF/BCF format 🧬 This is the main character. At least one of --vcf --bed --cov is REQUIRED, so don't skip it bestie 💀
• --bed quantifications.bed.gz — Molecular phenotype quantifications, in BED format 📊 At least one of --vcf --bed --cov is REQUIRED.
• --cov covariates.txt — Covariates data 🌈 At least one of --vcf --bed --cov is REQUIRED.
• --out filename_prefix — The output file name prefix 🎀 This one is REQUIRED, no exceptions.
• --region chr:start-end — The genomic region you want processed 🗺️ For example chr4:12334456-16334456, or chr5.

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🧁 OUTPUT FILES 🧁

• .content.txt.gz — A flat file with samples in rows and all the extracted variables in columns 🫧
• .header.txt — The genomic locations of the extracted variables 📍

🍓 EXAMPLE 🍓

Extract genotypes, gene quantifications, and covariates from a certain region, and it's giving chef's kiss 🤌

QTLtools extract --vcf genotypes.chr22.vcf.gz --bed
genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz
--region chr22:17000000-18000000 --out extract_output

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🔗 SEE ALSO 🔗

• QTLtools(1) — the big sibling 👯
• QTLtools website: <https://qtltools.github.io/qtltools> 🌐

🐛 BUGS 🐛

💀 Trigger warning, bestie. Versions up to and including 1.2 suffer from a bug in reading missing genotypes in VCF/BCF files. This bug affects variants with a DS field in their genotype's FORMAT and have a missing genotype (DS field is .) in one of the samples. When that happens, genotypes for all the samples are set to missing, which effectively removes that variant from the analyses 😭

Please submit bugs to <https://github.com/qtltools/qtltools> 🙏

📚 CITATION 📚

If you're citing this, the paper is giving academic queen energy 👑 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 👩‍💻

The brains behind it are Olivier Delaneau (olivier.delaneau@gmail.com) and Halit Ongen (halitongen@gmail.com) 🧠💖

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Okay that's the tea ☕ This was QTLtools-v1.3, dated 06 May 2020, filed under QTLtools-extract(1) forever 🦋 Love you, bestie 🫶💅