Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel
Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"
| File | Description |
|---|---|
| 1_QC.sh | step 1: perform qc check of the raw files |
| 2_trim.sh | step 2: perform trimming of the adapters on the raw files |
| 3_dm3_map_dedupl.sh | step 3: perform mapping to dm3 (for genotyping) |
| 4_dm3_getMap_stats.sh | step 4: check the quality of the maping on dm3 |
| 5_dm3_HaplotypeCaller.sh | step 5: perform calling of variants with haplotype caller, create gvcf |
| 6_dm3_GenotypeGVCF.sh | step 6: perform merging of raw gvcf with genotypegvcfs |
| 7_dm3_GenotypeWithR.sh | step 7: perform genotyping with use of custom r script |
| 7a_dm3_GenotypeGVCF.R | step 7: custom r script to perform genotyping |
| 8_dm6_map_dedupl_dm6.sh | step 8: perform mapping to dm6 & simultaniously correct genotypes |
| 9_dm6_getMap_stats.sh | step 9: check the quality of the maping on dm6 |
| 10_dm6_merge_BeversData.sh | step 10: merge mitochandrial gvcfs into one |
| 11_dm6_5950_5975_repeats.sh | step 11: extract reads mapping to the intergenic repeat region of the mitochondrial genome |
| 11A_Heteroplasmy.py | step 12: perform calculations of heteroplasmy |
| 12_Heteroplasmy.sh | step 12: perform calculations of heteroplasmy |
| 13_parse_nuclVars_for_GRD.sh | step 13: move dgrp2 vcf from dm3 to dm6, select variants by maf |
| 14_GRDs.sh | step 14: detect GRDs |
| 14a_GRDs.R | step 14: custom r script to detect GRDs |
| 15_annotate_GRD.sh | step 15: perform annotation of GRDs with use of snpeff |
| 16_functions.R | source file for the functions used in r scripts |
| 17_baseAnalysis.R | base analysis of the variation in mitochondrial genomes of dgrps |
| 18_compToRich_richGenome.R | comparison of the variants from this study to the previously published one |
| 19_heteroplasmy.R | post-processing of the heteroplasmy detection results |
| 20_GRD_postProc.R | post-processing of the GRDs |
| 21_parse_PhenoDB_MitoVcf_forGWAS.R | parsing of the data base of the phenotypes for further use in GWAS |
| 22_GWAS_Haplogroups.R | GWAS on mitochondrial haplogroups |
| 23_GRD_phenotypes.R | association of GRDs with phenotypes |
| Comparison to Richardson | folder containing scripts used for the comparison to the Richardson study |
| MitoRepeats | java source code used to process reads falling into repetitive region of mitochondrial genome |
| NUMTS | folder containing scripts used for the detection and quantification of NUMTs |