SNP_caller_benchmarking

SIMULATIONS FOLDER
1. demography_simulations.sh	#For running the simulations under the joint demographic model and getting the bam and the mpileup files
2. neutral_simulations.sh	#For running the simulations under the SNM and getting the bam and the mpileup files
3. mstatspop_simulations.sh	#For computing the Number of SNPs, SFS and the SNP Frequency of simulated data
4. mapgd_simulations.sh	#For calling SNPs using MAPGD with three different thresholds for the log-likelihood ratio (LLR) test
5. varscan2_simulations.sh	#For calling SNPs using VarScan2 and filtering the SNPs with different cross-sample P-values
6. snape1_simulations.sh	#For calling SNPs using SNAPE with flat prior and filtering the SNPs with P > 0.90
7. snape2_simulations.sh	#For calling SNPs using SNAPE with informative prior and filtering the SNPs with P > 0.90
8. poolsnp1_simulations.sh	#For calling SNPs using PoolSNP with miss-fraction = 0.1
9. poolsnp2_simulations.sh	#For calling SNPs using PoolSNP with miss-fraction = 0.8

DROSOPHILA DGRPs FOLDER
1. STRAINS FOLDER
1.1. mapping_strains.sh	#For trimming, mapping and getting the bam and the mpileup files for each DGRP strain
1.2. angsd4ngsd.sh	#For estimate the genotype likelihoods for each site of each DGRP strain to calculate their inbreeding coefficient
1.3. ngsd.sh	#For estimate the inbreeding coefficient of each DGRP strain using NGSD
1.4. angsd.sh	#For calling biallelic SNPs using ANGSD taking into account the inbreeding coefficients of each strain
2. POOLS FOLDER
2.1. mapping_pool_ral.sh	#For trimming, mapping and getting the bam and the mpileup files for each pool of DGRP strains
2.2. mapgd_pool_ral.sh	#For calling SNPs using MAPGD with three different thresholds for the log-likelihood ratio (LLR) test in each pool of DGRP strains
2.3. varscan2_pool_ral.sh	#For calling SNPs using VarScan2 and filtering the SNPs with different cross-sample P-values in each pool of DGRP strains
2.4. varscan2_joint_pool_ral.sh	#For calling SNPs using VarScan2 and filtering the SNPs with different cross-sample P-values in pools of DGRP strains joint variant calling option
2.5. snape1_pool_ral.sh	#For calling SNPs using SNAPE with flat prior and filtering the SNPs with P > 0.90 in each pool of DGRP strains
2.6. snape2_pool_ral.sh	#For calling SNPs using SNAPE with informative prior and filtering the SNPs with P > 0.90 in each pool of DGRP strains
2.7. poolsnp_pool_ral.sh	#For calling SNPs using PoolSNP in each pool of DGRP strains
2.8. poolsnp_joint_pools_ral.sh	#For calling SNPs using PoolSNP in pools of DGRP strains joint variant calling option with different values of miss-fraction