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How to run Regulatory Trait Cconcordance (RTC)?

RTC is XXX. To illustrate this, first download the example data below and go through the two steps; 1. permutation pass and 2. run RTC.

The phenotype data matrix for chr22 on 358 samples: BED / index
The genotype data matrix for chr22 on 358 samples: BED / index
The covariate data matrix on 358 samples: TXT

Step1: Run the permutation pass

This can be done quickly using 4 threads as follows:


		for j in $(seq 1 16); do

		  echo "cis --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --permute 200 --chunk $j 16 --out permutations_$j\_16.txt";

		done | xargs -P4 -n14 QTLtools

Then, cat all chunks together and run FDR correction:


		cat permutations_*.txt | gzip -c > permutations_all.txt.gz

		Rscript ./script/runFDR_cis.R permutations_all.txt.gz 0.05 permutations_all

From this, you get all your significant hits in permutations_all.significant.txt and you're ready to go to the next step.

Required files for RTC

For this step, you actually need two additionnal files:

Recombination hotspots that can can find here for b37: BED
The coordinates of the GWAS hits you want to overlap with QTLs. Example for chr22: TXT

The two files look like this:


		head hotspots_b37_hg19.bed

		1	1020078	1031078	11000

		1	1872839	1881839	9000

		1	2031839	2035839	4000

		1	2141839	2147839	6000

		1	2214839	2221839	7000

		1	2299839	2303839	4000

		1	2322839	2326839	4000

		1	2338839	2357839	19000

		1	2362839	2369839	7000

		1	2403839	2408839	5000

Columns here correspond to (only the first three columns are used):

1. Chromosome
2. Start (0-based)
3. End (1-based)
4. Length


		head GWAS.b37.txt

		1_1005806 Body

		1_1079198 Other

		1_1247494 Digestive

		1_1723031 Body

		1_2069172 Body

		1_2069681 Biological

		1_2205581 Other

		1_2387101 Neurological

		1_2392648 Other

		1_2452979 Other

Columns here correspond to (only the first column is used):

1. GWAS variants to test. These MUST correspond to the variants in your VCF file
2. Other information

Step2: Run RTC

To run RTC on all the files presented so far, use:


		QTLtools rtc --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --hotspot hotspots_b37_hg19.bed --gwas-cis GWAS.b37.txt permutations_all.significant.txt --normal --out rtc_results.txt

This step can be tuned using the following options:

--conditional: to run RTC with independent conditional eQTLs

This command produces the output file rtc_results.txt:


		head rtc_results.txt

		22_17597462 22_17620429 ENSG00000069998.8 ENSG00000069998.8 chr22 17597462 0 chr22 17620429 0 chr22 17646177 22967 48715 64959 64959 17583447 17666446 300 0.993333 NA 0.285641

		22_17597462 22_17587975 ENSG00000183307.3 ENSG00000183307.3 chr22 17597462 0 chr22 17587975 0 chr22 17602257 9487 4795 64959 64959 17583447 17666446 300 0.12 NA 0.0423723

		22_18283247 22_18261544 ENSG00000269220.1 ENSG00000269220.1 chr22 18283247 0 chr22 18261544 0 chr22 18260088 21703 23159 64978 64978 18251447 18283446 48 0.395833 NA 0.00236583

		22_18439958 22_18483388 ENSG00000093100.13 ENSG00000093100.13 chr22 18439958 0 chr22 18483388 0 chr22 18294263 43430 145695 64987 64987 18382447 18485446 325 0.483077 NA 0.236648

		22_18448113 22_18483388 ENSG00000093100.13 ENSG00000093100.13 chr22 18448113 0 chr22 18483388 0 chr22 18294263 35275 153850 64987 64987 18382447 18485446 325 0.483077 NA 0.236648

		22_18439958 22_18483388 ENSG00000243156.3 ENSG00000243156.3 chr22 18439958 0 chr22 18483388 0 chr22 18507325 43430 67367 64987 64987 18382447 18485446 325 0.483077 NA 0.236648

		22_18448113 22_18483388 ENSG00000243156.3 ENSG00000243156.3 chr22 18448113 0 chr22 18483388 0 chr22 18507325 35275 59212 64987 64987 18382447 18485446 325 0.483077 NA 0.236648

		22_19154522 22_19166680 ENSG00000100075.5 ENSG00000100075.5 chr22 19154522 0 chr22 19166680 0 chr22 19166343 12158 11821 65005 65005 19147447 19274446 277 0.920578 NA 0.887379

		22_19156117 22_19166680 ENSG00000100075.5 ENSG00000100075.5 chr22 19156117 0 chr22 19166680 0 chr22 19166343 10563 10226 65005 65005 19147447 19274446 277 0.906137 NA 0.745216

Description of the columns in the output file:

1. GWAS variant
2. eQTL variant
3. Gene
4. Gene Group
5. GWAS variant chromosome
6. GWAS variant position
7. GWAS variant rank
8. eQTL variant chromosome
9. eQTL variant position
10. eQTL variant rank
11. Gene chromosome
12. Gene position
13. Distance between variants
14. Distance between GWAS and phenotype
15. GWAS variant's region index
16. eQTL variant's region index
17. Region start
18. Region end
19. Number of variants in the region
20. RTC
21. D prime
22. R squared

Monday 11th July 2016