| 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 |