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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

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