QTLtools-fdensity

Section: Bioinformatics tools (1)
Updated: 06 May 2020
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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

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)

This document was created by man2html, using the manual pages.
Time: 14:11:25 GMT, August 24, 2020

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.

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