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ngsPool_assessment

Introduction

This project aims to compare the software ngsPool with commonly used software for Pooled-seq data such as Popoolation2, Snape and VarScan

For a full description and installation of the software ngsPool, visit the project page: https://github.com/mfumagalli/ngsJulia.git

Installation

Annotation of scripts

1. Scripts and functions

1.1 scripts for simulating mpileup

  • simulMpileup.R # original script quoted from the repository: SamueleSoraggi/HMMploidy
  • simulMpileup_qqVector.R # modified to simulate mpileup based on fixed Site frequency spectrum
  • simulMpileup_qq.R # modified to simulate mpileup based on fixed Minor allele frequency (MAF)

1.2 functions for Downstream analysis

  • mannual_output.jl # annotation of each column of output file of 4 programs (mannual for func_read_standard.jl)
  • func_read_standard.jl # read the minor allele frequency (MAF) estimation from the output file of programs
  • func_analysis_standard.jl # standardized functions for comparing by plotting

2. Script for estimating real data

  • real_data_pipeline # pipeline in bash script to get the estimation of MAF from real data (FASTQ file)

(Ref: Fracassetti M, Griffin PC, Willi Y. 2015. Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata. PLoS One. 10:e0140462. doi: 10.1371/journal.pone.0140462.)

3. Comparing programs (linux command script writing + analysis in one file) using real and simulated data

3.1 Test with different simulated data

  • compare_power_qqVector.jl # calculated power and FPR of SNP calling using simulated data with fixed expected Minor allele frequency (using simulMpileup_qq.R)
  • compare_power_sample.jl #calculated power and FPR of SNP calling using simulated data with sampled SFS (using simulMpileup.R: expected minor allele frequency is sampled from sampled Site Frequency Spectrum)

3.2 Exploring the setting of program

  • compare3estimates_ngsPool.jl # compare 3 estimates of ngsPool: maximum likelihood (GSS), maximum likelihood (SFS), expected estimate
  • compare_Snape.jl # exploring the setting of Snape (i.e. infuence of informative prior and flat prior MAF)
  • compare_ngsPool_snape.jl # compare the SNP calling by two software at different singificance levels
  • compare_snape_varscan.jl