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Enhanced version of the FastQTL QTL mapper

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FastQTL

This repository contains a modified version of the FastQTL QTL mapping software, with the following enhancements:

  1. Options for filtering by minor allele frequency and minor allele sample count
  2. Python wrapper for multi-threaded execution
  3. Calculation of q-values (Storey) for FDR estimation (requires R)
  4. Minor allele information reported in output

For documentation and the original version, see: http://fastqtl.sourceforge.net/

Running multi-threaded analyses

Nominal pass:

run_FastQTL_threaded.py ${genotypes}.vcf.gz ${phenotypes}.bed.gz ${prefix} --covariates ${covariates}.txt.gz --window 1e6 --ma_sample_threshold 10 --maf_threshold 0.01 --chunks 100 --threads 10

Permutation pass:

run_FastQTL_threaded.py ${genotypes}.vcf.gz ${phenotypes}.bed.gz ${prefix} --covariates ${covariates}.txt.gz --permute 1000 10000 --window 1e6 --ma_sample_threshold 10 --maf_threshold 0.01 --chunks 100 --threads 10

These minor allele filters result in inclusion of genotypes with minor allele frequency ≥ 0.01 and with at least 10 samples containing the minor allele.

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Enhanced version of the FastQTL QTL mapper

http://fastqtl.sourceforge.net

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