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Calculating stats on real data
Ariella Gladstein edited this page Dec 22, 2018
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1 revision
Use the script main_function_realdata_M23.py to calculate summary stats on one chromosome. It takes 6 arguments:
- chromosome number
- directory with real data
- Genome (CGI or 1000 Genomes) of HapMap pops file name (.tped format)
- Pseudo array data of HapMap pops file name (.tped format)
- Array data of AJ, Jews, Middle Eastern pops file name (.tped format)
- Germline input file (.ped or .map format)
e.g.:
python main_function_real_data_M23.py 1 /rsgrps/mfh/agladstein/ABC_data/chr1 ALL.atDNA.biAllelicSNPnoDI.genotypes_maf0.005_YRI9_CEU9_CHB4_chr1.tped ALL.atDNA.biAllelicSNPnoDI.genotypes_maf0.005_YRI9_CEU9_CHB4_hg18_Behar_HGDP_FtDNA_chr1.tped Behar_HGDP_FtDNA_Jews_MidEast_subset_chr1.tped Behar_HGDP_FtDNA_Jews_MidEast_subset_YRI9_CEU9_CHB4_chr1.ped