I'd like to use our eQTL data from monocytes. I ran a genome-wide eQTL analysis using QTLtools and permuted the results. I've read your instructions regarding conversion to BESD-format, but how can I best proceed with output from a permutation run using QTLtools?
I assume this result was from the nominal run not from a permutation run.
The columns for a nominal run are: 1. The phenotype ID 2. The chromosome ID of the phenotype 3. The start position of the phenotype 4. The end position of the phenotype 5. The strand orientation of the phenotype 6. The total number of variants tested in cis 7. The distance between the phenotype and the tested variant (accounting for strand orientation) 8. The ID of the tested variant 9. The chromosome ID of the variant 10. The start position of the variant 11. The end position of the variant 12. The nominal P-value of association between the variant and the phenotype 13. The corresponding regression slope 14. A binary flag equal to 1 is the variant is the top variant in cis
Did I miss something?
We are coding the functions to transform these QTLtoos formats to BESD format. Would be ready soon.