Genotype processing

Last updated: 2019-06-11

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Knit directory: apaQTL/analysis/

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File	Version	Author	Date	Message
Rmd	abd1ae9	brimittleman	2019-06-11	add geno proc info

Genotyes used for Li et al 2016, available at http://eqtl.uchicago.edu/jointLCL/genotypesYRI.gen.txt.gz

I need to add NA in front on the individual names and remove the chr in front of the chromosome. After I have completed this I can separate the files by chromosome.

The files are in /project2/gilad/briana/li_genotypes/

python processYRIgen.py

Keep only my individuals (53 of the 54 (19092 not in file))

module load vcftools
vcftools --vcf /project2/gilad/briana/li_genotypes/genotypesYRI.gen.proc.vcf --keep /project2/gilad/briana/li_genotypes/SAMPLE.txt  --recode --out genotypesYRI.gen.proc.keep.vcf

I will write a python script to remove snps that dont make it to MAF 5%. To do this I will write a script that adds up all of the dosages and checks if it exceeds .05.

python keep5perMAF.py

Next I will separate by chromosome:

sbatch run_sepgenobychrom.sh

bgzip and index each file:

sbatch tabixSNPS.sh

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.3.0 Rcpp_1.0.0      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.25.2    magrittr_1.5    evaluate_0.12  
 [9] stringi_1.2.4   fs_1.2.6        whisker_0.3-2   rmarkdown_1.10 
[13] tools_3.5.1     stringr_1.3.1   glue_1.3.0      yaml_2.2.0     
[17] compiler_3.5.1  htmltools_0.3.6 knitr_1.20

Genotype processing

Briana Mittleman

6/11/2019