QKcartographer

A set of scripts for processing output from QTL Cartographer. The current set of scripts are built around analyzing an F2 population. Adaptation for doubled-haploid and recombinant inbred line populations is current underway.

Scripts

QKcartographer_preprocess.py converts tabular flat text files into formatted input files for QTL Cartographer.

QKcartographer_permutations.py identifies experiment-wise thresholds based on permuted data sets from QTL Cartographer.

QKcartographer_visualization.py generates figures in PNG or postscript format for publication purposes.

QKcartographer_epistasis.py parses QTL Cartographer output files and permits curation of significant QTLs. Optional command to generate scripts for epistasis analysis with R/qtl.

QKcartographer_segregation.py analyzes the genetic map of a population and generates input files for generating a segregation distortion plot.

QKcartographer_phenotypes.py analyzes phenotypic data and generates input files for generating histograms and pairwise plots.

Example

Example of commands to run the set of scripts in Linux for a F2 population:

python QKcartographer_preprocess.py DxM SF2 DxM_phenotypic_data.txt DxM_genetic_map.txt

mkdir analysis

Rmap -A -i DxM_Rmap.inp -f 2 -V
Rcross -A -i DxM_Rcross.inp -V
SRmapqtl -A -i qtlcart.cro -t 1000 -u 5 -M 2 -V
Zmapqtl -A -i qtlcart.cro -t 1000 -M 6 -V
Eqtl -A -S 8 -H 10 -M 6 -V
mv qtlcart.eqt analysis/qtlcart_H0H1.eqt
Eqtl -A -S 8 -H 30 -M 6 -V
mv qtlcart.eqt analysis/qtlcart_H0H3.eqt
cp qtlcart.cro qtlcart.map qtlcart.sr qtlcart.z analysis/
rm qtlcart.sr qtlcart.z

bash permutations.sh

python QKcartographer_permutations.py DxM 0.95 1000
python QKcartographer_visualization.py DxM SF2 0.95
python QKcartographer_epistasis.py SF2 0.95

Example of commands to run the set of scripts in Linux for a DH population:

python QKcartographer_preprocess.py SxGP RI0 SxGP_phenotypic_data.txt SxGP_genetic_map.txt

mkdir analysis

Rmap -A -i SxGP_Rmap.inp -f 2 -V
Rcross -A -i SxGP_Rcross.inp -V
SRmapqtl -A -i qtlcart.cro -t 1000 -u 5 -M 2 -V
Zmapqtl -A -i qtlcart.cro -t 1000 -M 6 -V
Eqtl -A -S 8 -H 10 -M 6 -V
mv qtlcart.eqt analysis/qtlcart_H0H1.eqt
cp qtlcart.cro qtlcart.map qtlcart.sr qtlcart.z analysis/
rm qtlcart.sr qtlcart.z

bash permutations.sh

python QKcartographer_permutations.py SxGP 0.95 1000
python QKcartographer_visualization.py SxGP RI0 0.95
python QKcartographer_epistasis.py RI0 0.95

Both examples use a genetic map with cM positions generated using the Kosambi function.

Supported population type

Design	Code	Example	Description
Backcross i population	Bi	B1	Backcrossed once to mother
Fi population	SFi	SF2	F2 population
Doubled haploid population	RI0	RI0	DH population
Recombinant inbred line population	RI1	RI1	RIL population

Permutations

Permutations for composite interval mapping can be performed using the following bash shell commands:

mkdir permutations

for ((  i = 0 ;  i < 1000;  i++  ))
do
  ~/bin/Prune -A -i qtlcart.cro -b 2 -t 100 -V
  ~/bin/SRmapqtl -A -i qtlcart.crb -t 100 -u 5 -M 2 -V
  ~/bin/Zmapqtl -A -i qtlcart.crb -t 1000 -M 6 -V
  mv qtlcart.z permutations/qtlcart_$i.z
done

In this case, permutations are performed with reselection, where SRmapqtl is ran on each individual permuted data set (see Lauter et al. (2008) The Plant Genome http://dx.doi.org/10.3835/plantgenome2008.06.0385).

For interval mapping, the bash shell commands are the following:

mkdir permutations

for ((  i = 0 ;  i < 1000;  i++  ))
do
  ~/bin/Prune -A -i qtlcart.cro -b 2 -t 100 -V
  ~/bin/Zmapqtl -A -i qtlcart.crb -t 1000 -M 3 -V
  mv qtlcart.z permutations/qtlcart_$i.z
done