tutorials:population-diversity:snp-chips
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tutorials:population-diversity:snp-chips [2020/09/21 10:40] – [Data analysis workflow with Plink 1.9] bngina | tutorials:population-diversity:snp-chips [2020/09/22 10:21] (current) – [Data analysis workflow with Plink 1.9] bngina | ||
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- | ##this creats | + | </ |
+ | Above creates | ||
+ | *// | ||
+ | *// | ||
+ | | ||
+ | |||
+ | Now we use the created binary files, indicated to plink using '' | ||
+ | |||
+ | -Look a the individuals with missing data and SNPs not typed in all the individuals | ||
+ | |||
+ | < | ||
+ | |||
+ | |||
+ | |||
+ | ######### summary statistics ######## | ||
+ | |||
+ | # | ||
+ | |||
+ | plink --bfile ${out}/ | ||
+ | --out ${out}/ | ||
+ | | ||
</ | </ | ||
+ | This creates two files. | ||
+ | *// | ||
+ | *// | ||
+ | #The missing information found in the '' | ||
+ | < | ||
+ | FID IID MISS_PHENO | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | 10 | ||
+ | </ | ||
+ | |||
+ | The information in each header is as follows; | ||
+ | < | ||
+ | FID Family ID | ||
+ | IID Individual ID | ||
+ | MISS_PHENO | ||
+ | N_MISS | ||
+ | N_GENO | ||
+ | F_MISS | ||
+ | </ | ||
+ | |||
+ | The information found in the '' | ||
+ | < | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | </ | ||
+ | |||
+ | The information in each column is as follows; | ||
+ | < | ||
+ | SNP SNP identifier | ||
+ | CHR Chromosome number | ||
+ | N_MISS | ||
+ | N_GENO | ||
+ | F_MISS | ||
+ | </ | ||
+ | |||
+ | We can generate a file with filters added for the rate missing data in individuals '' | ||
+ | |||
+ | The thresholds for these filters should be adjusted accordingly to the different data sets. | ||
+ | |||
+ | < | ||
+ | |||
+ | #### filter data ### | ||
+ | |||
+ | plink --file ${file} \ | ||
+ | | ||
+ | --maf 0.01\ #SNPs with less than 1% minor allele frequencies | ||
+ | | ||
+ | --out ${out}/ | ||
+ | | ||
+ | |||
+ | </ | ||
===== Data analysis workflow with R and adegenet ===== | ===== Data analysis workflow with R and adegenet ===== | ||
tutorials/population-diversity/snp-chips.txt · Last modified: 2020/09/22 10:21 by bngina