QTL Workflow

QTL mapping of drug response in a Plasmodium falciparum genetic cross (Dd2 × HB3), followed by a search for genes and mutations inside the QTL intervals using the cross’s VCF. Written in R with the qtl package.

• Contact: Tarrick Qahash (tqahash@nd.edu)
• Code: code/QTL_Code.R
• Data: data/*.csv (linkage map and phenotypes) and the full VCF, split into two parts to fit GitHub’s file limit. Rebuild it with scripts/restore-vcf.sh.

Minimal run

From this directory on CRC:

module load R/4.4.0/gcc/11.5.0
mkdir -p .R-library results
Rscript -e 'install.packages("qtl", lib=".R-library", repos="https://cloud.r-project.org")'
Rscript scripts/minimal-run.R > results/minimal-run.log 2>&1

minimal-run.R does one single-trait scan from the original script (the CQ..IC50. phenotype) with only 10 permutations. scripts/permutation-run.R runs the same scan with the original 1,000. Neither covers the two-dimensional scans, the loop over all phenotypes, or the VCF part of QTL_Code.R.

The input produces warnings about missing genotypes and duplicate marker positions on chromosome 13. They are expected.