WGS analysis of the Dummerstorf mouse lines

This repository contains the scripts used to analyse whole genome sequencing data of the Dummerstorf mouse lines. The analysis starts from raw sequences and ends with multiple analysis to characterize each mice line in terms of genetic differentiation, admixture, genomewide similarities and structural variation.

Name		Name	Last commit message	Last commit date
Latest commit History 14 Commits
.gitignore		.gitignore
01_qc_before_read_cleaning.sh		01_qc_before_read_cleaning.sh
02_read_cleaning.sh		02_read_cleaning.sh
03_qc_after_read_cleaning.sh		03_qc_after_read_cleaning.sh
04_mapping_to_reference.sh		04_mapping_to_reference.sh
05_bam_prep_AddOrReplaceReadGroups.sh		05_bam_prep_AddOrReplaceReadGroups.sh
06_bam_prep_MergeSamFiles.sh		06_bam_prep_MergeSamFiles.sh
07_bam_prep_SortSam.sh		07_bam_prep_SortSam.sh
08_bam_prep_MarkDuplicates.sh		08_bam_prep_MarkDuplicates.sh
09_CollectWgsMetrics.sh		09_CollectWgsMetrics.sh
10_BQSR.sh		10_BQSR.sh
11_HaplotypeCaller.sh		11_HaplotypeCaller.sh
12_GenomicsDBImport.sh		12_GenomicsDBImport.sh
13_GenotypeGVCFs.sh		13_GenotypeGVCFs.sh
14_concatenate_and_validate.sh		14_concatenate_and_validate.sh
15_extract_SNPs.sh		15_extract_SNPs.sh
16_extract_INDELs.sh		16_extract_INDELs.sh
17_VariantsToTable_SNPs.sh		17_VariantsToTable_SNPs.sh
18_VariantsToTable_INDELs.sh		18_VariantsToTable_INDELs.sh
19_extract_good_sites.R		19_extract_good_sites.R
20_variants_for_training.sh		20_variants_for_training.sh
21_VariantRecalibration_SNPs.sh		21_VariantRecalibration_SNPs.sh
22_VariantRecalibration_SNPs.sh		22_VariantRecalibration_SNPs.sh
23_ApplyVQSR_SNPs.sh		23_ApplyVQSR_SNPs.sh
24_ApplyVQSR_INDELs.sh		24_ApplyVQSR_INDELs.sh
25_SelectVariants.sh		25_SelectVariants.sh
26_add_missingness.sh		26_add_missingness.sh
27_get_intervals.R		27_get_intervals.R
28_generate_final_VCF.sh		28_generate_final_VCF.sh
29_variant_annotatation.sh		29_variant_annotatation.sh
30_VCF_to_GDS.R		30_VCF_to_GDS.R
31_PCA.R		31_PCA.R
32_hierarchical_clustering.R		32_hierarchical_clustering.R
33_vcf_to_plink_bed.sh		33_vcf_to_plink_bed.sh
34_admixture.sh		34_admixture.sh
35_thin_VCF.sh		35_thin_VCF.sh
36_split_thinned_vcf_by_population.sh		36_split_thinned_vcf_by_population.sh
37_LD_decay_r2.sh		37_LD_decay_r2.sh
38_LD_decay_fig.R		38_LD_decay_fig.R
39_alternative_allele_freq.sh		39_alternative_allele_freq.sh
40_prep_data_for_ROHs.sh		40_prep_data_for_ROHs.sh
41_ROHs.sh		41_ROHs.sh
42_windowed_fst.sh		42_windowed_fst.sh
43_regions_of_distinct_genetic_differentiation.R		43_regions_of_distinct_genetic_differentiation.R
44_enrichment_analysis.R		44_enrichment_analysis.R
45_nucleotide_diversity.sh		45_nucleotide_diversity.sh
46_SV_calling_pipeline.snakefile		46_SV_calling_pipeline.snakefile
47_SV_annotation.snakefile		47_SV_annotation.snakefile
48_SV_counts_plot.Rmd		48_SV_counts_plot.Rmd
README.md		README.md

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WGS analysis of the Dummerstorf mouse lines

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