This page is outdated, please also see the man page.

How to run QTLtools

QTLtools contain the following multiple functionalities:

• [bamstat] to control the quality of the sequence data
• [match] to ensure good matching between sequence and genotype data
• [quan] to quantify gene expression
• [pca] to perform PCA on phenotype and genotype data
• [cis] to discover QTL in cis via a nominal pass of association
• [cis] to discover QTL in cis via a permutation pass of association
• [cis] to discover multiple QTLs per phenotype in cis using a conditional pass
• [trans] to discover QTL in trans using a full permutation pass
• [trans] to discover QTL in trans using an approximated permutation pass
• [fdensity] to measure functional annotation density around QTLs
• [fenrich] to measure enrichment of QTLs within annotations
• [rtc] to overlap QTLs with GWAS hits

To get the full list of available nodes, use:

QTLtools QTLtools is under constant development and multiple modes are experimental. We do not recommend to use a mode that is not described in this online documentation

To run a particular functionality, you need to combine QTLtools with the appropriate mode. For instance, to run bamstat, use:

QTLtools bamstat ...

Where ... stands for all options unique to the mode used. To get a full list of available options with short description, run:

QTLtools bamstat --help

QTLtools allows dumping the screen output in a LOG file. To do so, use:

QTLtools mode ... --log myScreenOutput.log

For any procedure based on random permutations, you can specify the seed in order to get a different random number sequence or to reproduce a particular experiment. To do so, use:

QTLtools mode ... --seed 12345