QTLtools fdensity - Functional density around molecular QTLs
QTLtools fdensity --qtl significant_genes.bed --bed
TFs.encode.bed.gz --out output.txt [OPTIONS]
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.
- --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
- --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) |
- --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 |
- 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
QTLtools(1)
QTLtools website: <
https://qtltools.github.io/qtltools>
Please submit bugs to <
https://github.com/qtltools/qtltools>
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>
Olivier Delaneau (
[email protected]), Halit Ongen
(
[email protected])