Some small useful tools
Input selected (sorted) pileup file
Output the raw file of final R data.table with column
dataset chrom site sample coverage bq mq (snp)
This code will produce R code for region analysis.
Each line of input file starts as this:
"chr18:1000-100000"
The output R code depends on other R data.
Filter out special sites with specified ratio of non-reference.
Input selected (sorted) pileup file
Output site list file
Filter out special sites based on pilup files and site list files.
Input orgin pileup files and site list files
Output selected pileup files (and use linux command to sort)
Calculate single sites' R and N's ratio and bq
Input filtered single site pileup file
Ooutput result file
Have some problem. Replace by BuildData.java and other R scripts.
Continue the work of BuildData.java. Produce fina_data datatable.
Test the process of GeMS's EM algorithm. Depend on em.R which is the core functions of GeMS.
Calculate TPR and HM according to quntile and property(mq, bq, coverage) for each chromosome
Calculate TPR and HM according to quntile and property(mq, bq, coverage) for GiaB(upenn) dataset