RandomSNPsQTL
1 Introduction
We provide a SNP that allows to randomly picking the QTLs for the qt-mode and the qff-mode. As input the MimicrEE2 haplotypes are required.
The script allows for two options
- all selected SNPs may have the same effect size
- the selected SNPs may follow a distribution of effect sizes as provided in a file
Note this is quite similar to randomly picking the targets of selection for the w-mode [RandomSNPsWMode]
Requirements
First download the MimicrEE2 haplotypes https://sourceforge.net/projects/mimicree2/files/starvation_resistance/mimicree_format_dgrp_snps_X_chromosome.gz/download
Than download the script https://sourceforge.net/projects/mimicree2/files/scripts/pick-SNPs-QTL.py/download
the following parameters are important:
- --mimhap the MimicrEE2 haplotype file; may be zipped or unzipped
- --n the number of selected loci
- --f the minimum allele frequency; For example if --f 0.05 is provided all SNPs will have an allele frequency betwee 0.05 and 0.95
- --a the additive effect size of the selected SNPs (either --a or --effect-file needs to be provided)
- --d the dominance effect of the selected SNPs; default = 0.0
- --effect-file provide a file with the effect size distribution of the selected SNPs (this will override any values provided in --a or --d)
The script will first select all loci that fullfill the frequency criteria (thus having a minimum frequency of --f). Then it selects the requested number of loci randomly from this set. Finally it randomly chooses one of the two alleles at each SNPs as having the effect size a while the other allele has effect size -a.
2 Pick SNPs with identical additive effect size
python pick-SNPs-QTL.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --a 1.0 --d 0.0 > additive.txt
and we for example obtain the following output (cat additive.txt)
3L 12964331 C/T 1.0 0.0
3R 19601182 G/A 1.0 0.0
3R 24104354 A/C 1.0 0.0
3R 9187668 T/A 1.0 0.0
3L 2923043 T/G 1.0 0.0
2L 6614778 T/C 1.0 0.0
2L 18900183 G/C 1.0 0.0
2L 4326294 A/G 1.0 0.0
3R 6801867 T/G 1.0 0.0
3R 14995600 A/T 1.0 0.0
2R 14050081 T/C 1.0 0.0
3L 13393686 A/T 1.0 0.0
X 16430602 A/T 1.0 0.0
X 4327124 G/T 1.0 0.0
2L 2172947 T/A 1.0 0.0
2R 18124893 G/A 1.0 0.0
3L 17693433 G/T 1.0 0.0
3R 26933314 G/A 1.0 0.0
2L 15246918 A/G 1.0 0.0
3L 2598523 G/A 1.0 0.0
For details on this file format see [SelectedLoci]
3 Pick SNPs with an additive effect size drawn from a distribution
distribution of effect size
In order to randomly pick SNPs that follow some effect size distribution you have to provide a file containing the desired distribution of effect sizes.
The file needs to have two column and may have an arbitrary number of rows:
- column1: the addtive effect size
- column2: the dominance effect
For examle given the following content stored in file effectsizedistr.txt
1.0 0.0
1.5 0.0
1.0 0.0
1.1 0.0
1.2 0.0
1.2 0.0
1.0 0.0
1.0 0.0
The script will assign a random effect sizes to each selected SNPs. The effect size is drawn from this file by picking random rows with replacement.
Thus the combination of additive effect size and dominance effect as provided in the file will be maintained.
Based on this example most SNPs will have an additive effect 1.0, some have an additive effect of 1.2 and few will have an effect of 1.5. But all SNPs will have a dominance effect of 0.0.
pick the QTLs
With the following command we randomly pick the QTLs
python scripts/pick-SNPs-QTL.py --mimhap mimicree_format_dgrp_snps_X_chromosome.gz --n 20 --effect-file effectsizedistr.txt --f 0.05
and we obtain an output similar to this one
3L 18929259 T/A 1.2 0.0
2L 19698812 T/C 1.0 0.0
2L 7021887 G/A 1.0 0.0
2L 7617017 T/A 1.0 0.0
3L 348772 G/T 1.5 0.0
3L 15841049 G/T 1.2 0.0
3R 13789648 C/G 1.5 0.0
3R 6987528 C/T 1.0 0.0
3R 8719965 G/C 1.0 0.0
X 4412847 A/C 1.0 0.0
2L 17575441 A/G 1.0 0.0
3R 25068798 A/G 1.0 0.0
2R 13307602 T/A 1.0 0.0
2L 9058000 G/C 1.1 0.0
2L 13699585 G/T 1.2 0.0
X 16920825 G/C 1.1 0.0
3R 7001766 G/A 1.1 0.0
3L 8041494 T/A 1.0 0.0
2R 16534711 G/T 1.0 0.0
2R 7452620 G/A 1.5 0.0
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