505_unused.Rmd

Title: code that I didn't keep in the working code but might be useful late sometime 
========================================================

```{r}
# 6) filter using vcftool to get only biallelic SNPs
# extract_SNP.sh & extract_biallelic.sh 
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/extract_SNP.sh)  
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/extract_biallelic.sh) 
# output: 505_SNP_biallelic.gz 

# 7) filter based on MAF and Q 
# filtering_MAF_Q.sh 
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/filtering_MAF_Q.sh)
# output: 505_filtered_MAF_Q.gz 

# 8) calcaulate mean read depth across individuals
# calc_depth.sh
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/calc_depth.sh) calculate in R
# output: 505_filtered_MAF_Q.ldepth.mean 

# 9) filter based on read depth (after check mean and distribution of read depth, decide to use 5-500 as the threshold)
# filtering_depth.sh
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/filtering_depth.sh)
# output: 505_filtered_MAF_Q_depth.gz 

# 10) calculate missing rate (SNPs with less than median of missing rate should be filtered out) 
# calc_missingness.sh 
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/calc_missingness.sh)
# output: 505_filtered_MAF_Q_depth.imiss; 505_filtered_MAF_Q_depth.lmiss 

# 11) filter based on missing rate 
# filter_missingness.sh 
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/filtering_missingrate.sh)
# output: 505_filtered_MAF_Q_depth_missingness.gz 

# 12) calculate MAF, missing rate, depth, and LD... 
# calc.sh
# (https://github.com/leejimmy93/KIAT_whitney/blob/master/505/calc.sh)
# output: a lot of stats start with 505_filtered_MAF_Q_depth_missingness prefix 
```