RandHaps calculates the probability of SNPs encountering by chance
./RandHaps assoc_file map_file IBDlength rd
where:
assoc_file - associated SNPs from GRASP
map_file - Illumina 610k physical map range for each chromosome
IBDlength - length of IBD haplotype
rd - number of random haplotype pairs to be generated
head -5 assoc_file CHR POS 1 2260994 1 2434877 1 2445961 1 2446607 tail -5 assoc_file 22 50479977 22 50624404 22 50625988 22 50642332 22 50733265
cat map_file chr start end 1 742429 247177330 2 8856 242692820 3 38411 199308268 4 63508 191164126 5 91139 180642521 6 110391 170761395 7 140736 158812247 8 166818 146264218 9 36587 140147760 10 114767 135284293 11 189256 134445626 12 64079 132288869 13 18110262 114121252 14 19283777 106358708 15 18421386 100216154 16 37354 88677423 17 51088 78634366 18 59836 76116152 19 217034 63779291 20 11244 62382907 21 9993822 46909175 22 14884399 49524956
[email protected]
[email protected]
This tool was developed for
Ural Yunusbayev, Albert Valeev, Milyausha Yunusbaeva, Reedik Mägi, Mait Metspalu, Bayazit Yunusbayev. (2019). Reconstructing recent population history while mapping rare variants using haplotypes.