---
name: "QTLtools-fdensity"
section: "1"
platform: "linux"
package: "qtltools"
version: "1.3.1+dfsg-4+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/QTLtools-fdensity"
---

# QTLtools-fdensity(1)

Functional density around molecular QTLs

## NAME

QTLtools fdensity - Functional density around molecular QTLs

## SYNOPSIS

**QTLtools fdensity --qtl** *significant\_genes.bed* **--bed** *TFs.encode.bed.gz* **--out** *output.txt* *\[OPTIONS\]*

## DESCRIPTION

This mode measures the density of functional annotations around the genomic positions of molecular QTLs. The method is detailed in \<https://www.nature.com/articles/ncomms15452\>. In brief, we first enumerate all annotations within a given window around the molecular QTLs (by default 1 Mb). Then, we split this window into small bins (default 1 kb) and count the number of functional annotations overlapping each bin.  This produces an annotation count per bin that can be then plotted to see if there is any peak or depletion around the molQTLs.

## OPTIONS

- **--qtl *in.bed***

  List of QTLs of interest in BED format. REQUIRED.

- **--bed *functional\_annotation.bed.gz***

  Functional annotations in BED format. REQUIRED.

- **--out *output.txt***

  Output file. REQUIRED.

- **--window *integer***

  Window size around the molecular QTL position. DEFAULT=1000000

- **--bin *integer***

  Bin size in base pairs. DEFAULT=1000

## INPUT FILES

- **--qtl file**

  List of QTLs of interest. An example:

  1	15210	15211	1\_15211	ENSG00000227232.4	-

  1	735984	735985	1\_735985	ENSG00000177757.1	+

  1	735984	735985	1\_735985	ENSG00000240453.1	-

  1	739527	739528	1\_739528	ENSG00000237491.4	+

  The column definitions are:

  | | |
  | --- | --- |
  | 1 | The variant chromosome |
  | 2 | The variant's start position (**0-based**) |
  | 3 | The variant's end position (**1-based**) |
  | 4 | The variant ID |
  | 5 | The phenotype ID (**not used**) |
  | 6 | The phenotype's strand. |

- **--bed file**

  List of annotations in BED format. An example:

  1	254874	265487

  1	730984	735985

  1	734984	736585

  1	739527	748528

  The column definitions are:

  | | |
  | --- | --- |
  | 1 | Chromosome |
  | 2 | Start position (**0-based**) |
  | 3 | End position (**1-based**) |

## OUTPUT FILE

- **--out file**

  Space separated results output file detailing the enrichment with the following columns:

  | | |
  | --- | --- |
  | 1 | The start position of the bin |
  | 2 | The end position of the bin |
  | 3 | The number of associations in this bin |

## EXAMPLE

- 1

  You need to prepare a BED file containing the positions of the QTLs of interest. To do so, extract all significant hits at a given FDR threshold (e.g. 5%), and then transform the significant QTL list into a BED file:

-

  Rscript ./script/qtltools\_runFDR\_cis.R results.genes.full.txt.gz 0.05 results.genes

  cat results.genes.significant.txt \| awk '{ print $9, $10-1, $11, $8, $1, $5 }' \| tr ' ' '\\t' \| sort -k1,1V -k2,2g \> results.genes.significant.bed

- 2

  Measure the density using the following command:

-

  QTLtools fdensity --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt

## SEE ALSO

[*QTLtools*(1)](/QTLtools/1.md)

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)