├── .gitignore ├── Assignments ├── Backup │ ├── ProblemSet1 │ │ └── ProblemSet1.txt │ ├── ProblemSet2 │ │ └── ProblemSet2.txt │ ├── ProblemSet3 │ │ └── ProblemSet3.txt │ ├── ProblemSet4 │ │ └── ProblemSet4.txt │ └── ProblemSet5 │ │ └── ProblemSet5.txt ├── Old │ ├── PreQuiz_Session1.txt │ ├── Session1_Problemset.txt │ ├── Session2_Problemset.txt │ ├── Session3_Problemset.txt │ ├── Session4_Problemset.txt │ ├── Session5_Problemset.txt │ └── Session6_Problemset.txt ├── ProblemSet1 │ └── ProblemSet1.txt ├── ProblemSet2 │ └── ProblemSet2.txt ├── ProblemSet3 │ └── ProblemSet3.txt ├── ProblemSet4 │ └── ProblemSet4.txt └── ProblemSet5 │ └── ProblemSet5.txt ├── CaseInformation ├── BamSurgeonScripts │ ├── BamToSubRegionFastq.sh │ ├── InstallPrereqs.sh │ ├── MakeBamSurgeons.sh │ ├── RunBamSurgeon.sh │ ├── RunBamSurgeon_All.sh │ ├── RunBamSurgeon_slurm_case1.sh │ ├── RunBamSurgeon_slurm_case10.sh │ ├── RunBamSurgeon_slurm_case2.sh │ ├── RunBamSurgeon_slurm_case3.sh │ ├── RunBamSurgeon_slurm_case4.sh │ ├── RunBamSurgeon_slurm_case5.sh │ ├── RunBamSurgeon_slurm_case6.sh │ ├── RunBamSurgeon_slurm_case7.sh │ ├── RunBamSurgeon_slurm_case8.sh │ ├── RunBamSurgeon_slurm_case9.sh │ └── reference.sh ├── CaseFiles │ ├── Case1 │ │ ├── Case1.ped │ │ ├── Case1_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case10 │ │ ├── Case10.ped │ │ ├── Case10_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case2 │ │ ├── Case2.ped │ │ ├── Case2_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case3 │ │ ├── Case3.ped │ │ ├── Case3_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case4 │ │ ├── Case4.ped │ │ ├── Case4_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case5 │ │ ├── Case5.ped │ │ ├── Case5_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case6 │ │ ├── Case6.ped │ │ ├── Case6_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case7 │ │ ├── Case7.ped │ │ ├── Case7_Phenopacket.json │ │ └── PatientDescription.txt │ ├── Case8 │ │ ├── Case8.ped │ │ ├── Case8_Phenopacket.json │ │ └── PatientDescription.txt │ └── Case9 │ │ ├── Case9.ped │ │ ├── Case9_Phenopacket.json │ │ └── PatientDescription.txt ├── Exomiser │ ├── Case1 │ │ ├── Case1_exomiser.html │ │ ├── Case1_exomiser.json │ │ ├── Case1_exomiser_AD.genes.tsv │ │ ├── Case1_exomiser_AD.variants.tsv │ │ ├── Case1_exomiser_AD.vcf │ │ ├── Case1_exomiser_AR.genes.tsv │ │ ├── Case1_exomiser_AR.variants.tsv │ │ ├── Case1_exomiser_AR.vcf │ │ ├── Case1_exomiser_MT.genes.tsv │ │ ├── Case1_exomiser_MT.variants.tsv │ │ ├── Case1_exomiser_MT.vcf │ │ ├── Case1_exomiser_XD.genes.tsv │ │ ├── Case1_exomiser_XD.variants.tsv │ │ ├── Case1_exomiser_XD.vcf │ │ ├── Case1_exomiser_XR.genes.tsv │ │ ├── Case1_exomiser_XR.variants.tsv │ │ ├── Case1_exomiser_XR.vcf │ │ └── spring.log │ ├── Case10 │ │ ├── Case10_exomiser.html │ │ ├── Case10_exomiser.json │ │ ├── Case10_exomiser_AD.genes.tsv │ │ ├── Case10_exomiser_AD.variants.tsv │ │ ├── Case10_exomiser_AD.vcf │ │ ├── Case10_exomiser_AR.genes.tsv │ │ ├── Case10_exomiser_AR.variants.tsv │ │ ├── Case10_exomiser_AR.vcf │ │ ├── Case10_exomiser_MT.genes.tsv │ │ ├── Case10_exomiser_MT.variants.tsv │ │ ├── Case10_exomiser_MT.vcf │ │ ├── Case10_exomiser_XD.genes.tsv │ │ ├── Case10_exomiser_XD.variants.tsv │ │ ├── Case10_exomiser_XD.vcf │ │ ├── Case10_exomiser_XR.genes.tsv │ │ ├── Case10_exomiser_XR.variants.tsv │ │ ├── Case10_exomiser_XR.vcf │ │ └── spring.log │ ├── Case10_Exomiser.yml │ ├── Case1_Exomiser.yml │ ├── Case2 │ │ ├── Case2_exomiser.html │ │ ├── Case2_exomiser.json │ │ ├── Case2_exomiser_AD.genes.tsv │ │ ├── Case2_exomiser_AD.variants.tsv │ │ ├── Case2_exomiser_AD.vcf │ │ ├── Case2_exomiser_AR.genes.tsv │ │ ├── Case2_exomiser_AR.variants.tsv │ │ ├── Case2_exomiser_AR.vcf │ │ ├── Case2_exomiser_MT.genes.tsv │ │ ├── Case2_exomiser_MT.variants.tsv │ │ ├── Case2_exomiser_MT.vcf │ │ ├── Case2_exomiser_XD.genes.tsv │ │ ├── Case2_exomiser_XD.variants.tsv │ │ ├── Case2_exomiser_XD.vcf │ │ ├── Case2_exomiser_XR.genes.tsv │ │ ├── Case2_exomiser_XR.variants.tsv │ │ ├── Case2_exomiser_XR.vcf │ │ └── spring.log │ ├── Case2_Exomiser.yml │ ├── Case3 │ │ ├── Case3_exomiser.html │ │ ├── Case3_exomiser.json │ │ ├── Case3_exomiser_AD.genes.tsv │ │ ├── Case3_exomiser_AD.variants.tsv │ │ ├── Case3_exomiser_AD.vcf │ │ ├── Case3_exomiser_AR.genes.tsv │ │ ├── Case3_exomiser_AR.variants.tsv │ │ ├── Case3_exomiser_AR.vcf │ │ ├── Case3_exomiser_MT.genes.tsv │ │ ├── Case3_exomiser_MT.variants.tsv │ │ ├── Case3_exomiser_MT.vcf │ │ ├── Case3_exomiser_XD.genes.tsv │ │ ├── Case3_exomiser_XD.variants.tsv │ │ ├── Case3_exomiser_XD.vcf │ │ ├── Case3_exomiser_XR.genes.tsv │ │ ├── Case3_exomiser_XR.variants.tsv │ │ ├── Case3_exomiser_XR.vcf │ │ └── spring.log │ ├── Case3_Exomiser.yml │ ├── Case4 │ │ ├── Case4_exomiser.html │ │ ├── Case4_exomiser.json │ │ ├── Case4_exomiser_AD.genes.tsv │ │ ├── Case4_exomiser_AD.variants.tsv │ │ ├── Case4_exomiser_AD.vcf │ │ ├── Case4_exomiser_AR.genes.tsv │ │ ├── Case4_exomiser_AR.variants.tsv │ │ ├── Case4_exomiser_AR.vcf │ │ ├── Case4_exomiser_MT.genes.tsv │ │ ├── Case4_exomiser_MT.variants.tsv │ │ ├── Case4_exomiser_MT.vcf │ │ ├── Case4_exomiser_XD.genes.tsv │ │ ├── Case4_exomiser_XD.variants.tsv │ │ ├── Case4_exomiser_XD.vcf │ │ ├── Case4_exomiser_XR.genes.tsv │ │ ├── Case4_exomiser_XR.variants.tsv │ │ ├── Case4_exomiser_XR.vcf │ │ └── spring.log │ ├── Case4_Exomiser.yml │ ├── Case4_exomiser.html │ ├── Case4_exomiser.json │ ├── Case5 │ │ ├── Case5_exomiser.html │ │ ├── Case5_exomiser.json │ │ ├── Case5_exomiser_AD.genes.tsv │ │ ├── Case5_exomiser_AD.variants.tsv │ │ ├── Case5_exomiser_AD.vcf │ │ ├── Case5_exomiser_AR.genes.tsv │ │ ├── Case5_exomiser_AR.variants.tsv │ │ ├── Case5_exomiser_AR.vcf │ │ ├── Case5_exomiser_MT.genes.tsv │ │ ├── Case5_exomiser_MT.variants.tsv │ │ ├── Case5_exomiser_MT.vcf │ │ ├── Case5_exomiser_XD.genes.tsv │ │ ├── Case5_exomiser_XD.variants.tsv │ │ ├── Case5_exomiser_XD.vcf │ │ ├── Case5_exomiser_XR.genes.tsv │ │ ├── Case5_exomiser_XR.variants.tsv │ │ ├── Case5_exomiser_XR.vcf │ │ └── spring.log │ ├── Case5_Exomiser.yml │ ├── Case6 │ │ ├── Case6_exomiser.html │ │ ├── Case6_exomiser.json │ │ ├── Case6_exomiser_AD.genes.tsv │ │ ├── Case6_exomiser_AD.variants.tsv │ │ ├── Case6_exomiser_AD.vcf │ │ ├── Case6_exomiser_AR.genes.tsv │ │ ├── Case6_exomiser_AR.variants.tsv │ │ ├── Case6_exomiser_AR.vcf │ │ ├── Case6_exomiser_MT.genes.tsv │ │ ├── Case6_exomiser_MT.variants.tsv │ │ ├── Case6_exomiser_MT.vcf │ │ ├── Case6_exomiser_XD.genes.tsv │ │ ├── Case6_exomiser_XD.variants.tsv │ │ ├── Case6_exomiser_XD.vcf │ │ ├── Case6_exomiser_XR.genes.tsv │ │ ├── Case6_exomiser_XR.variants.tsv │ │ ├── Case6_exomiser_XR.vcf │ │ └── spring.log │ ├── Case6_Exomiser.yml │ ├── Case7 │ │ ├── Case7_exomiser.html │ │ ├── Case7_exomiser.json │ │ ├── Case7_exomiser_AD.genes.tsv │ │ ├── Case7_exomiser_AD.variants.tsv │ │ ├── Case7_exomiser_AD.vcf │ │ ├── Case7_exomiser_AR.genes.tsv │ │ ├── Case7_exomiser_AR.variants.tsv │ │ ├── Case7_exomiser_AR.vcf │ │ ├── Case7_exomiser_MT.genes.tsv │ │ ├── Case7_exomiser_MT.variants.tsv │ │ ├── Case7_exomiser_MT.vcf │ │ ├── Case7_exomiser_XD.genes.tsv │ │ ├── Case7_exomiser_XD.variants.tsv │ │ ├── Case7_exomiser_XD.vcf │ │ ├── Case7_exomiser_XR.genes.tsv │ │ ├── Case7_exomiser_XR.variants.tsv │ │ ├── Case7_exomiser_XR.vcf │ │ └── spring.log │ ├── Case7_Exomiser.yml │ ├── Case8 │ │ ├── Case8_exomiser.html │ │ ├── Case8_exomiser.json │ │ ├── Case8_exomiser_AD.genes.tsv │ │ ├── Case8_exomiser_AD.variants.tsv │ │ ├── Case8_exomiser_AD.vcf │ │ ├── Case8_exomiser_AR.genes.tsv │ │ ├── Case8_exomiser_AR.variants.tsv │ │ ├── Case8_exomiser_AR.vcf │ │ ├── Case8_exomiser_MT.genes.tsv │ │ ├── Case8_exomiser_MT.variants.tsv │ │ ├── Case8_exomiser_MT.vcf │ │ ├── Case8_exomiser_XD.genes.tsv │ │ ├── Case8_exomiser_XD.variants.tsv │ │ ├── Case8_exomiser_XD.vcf │ │ ├── Case8_exomiser_XR.genes.tsv │ │ ├── Case8_exomiser_XR.variants.tsv │ │ ├── Case8_exomiser_XR.vcf │ │ └── spring.log │ ├── Case8_Exomiser.yml │ ├── Case9 │ │ ├── Case9_exomiser.html │ │ ├── Case9_exomiser.json │ │ ├── Case9_exomiser_AD.genes.tsv │ │ ├── Case9_exomiser_AD.variants.tsv │ │ ├── Case9_exomiser_AD.vcf │ │ ├── Case9_exomiser_AR.genes.tsv │ │ ├── Case9_exomiser_AR.variants.tsv │ │ ├── Case9_exomiser_AR.vcf │ │ ├── Case9_exomiser_MT.genes.tsv │ │ ├── Case9_exomiser_MT.variants.tsv │ │ ├── Case9_exomiser_MT.vcf │ │ ├── Case9_exomiser_XD.genes.tsv │ │ ├── Case9_exomiser_XD.variants.tsv │ │ ├── Case9_exomiser_XD.vcf │ │ ├── Case9_exomiser_XR.genes.tsv │ │ ├── Case9_exomiser_XR.variants.tsv │ │ ├── Case9_exomiser_XR.vcf │ │ └── spring.log │ ├── Case9_Exomiser.yml │ ├── HTMLs │ │ ├── Case10_exomiser.html │ │ ├── Case1_exomiser.html │ │ ├── Case2_exomiser.html │ │ ├── Case3_exomiser.html │ │ ├── Case4_exomiser.html │ │ ├── Case5_exomiser.html │ │ ├── Case6_exomiser.html │ │ ├── Case7_exomiser.html │ │ ├── Case8_exomiser.html │ │ └── Case9_exomiser.html │ ├── RunExomiser_case1.sh │ ├── RunExomiser_case10.sh │ ├── RunExomiser_case2.sh │ ├── RunExomiser_case3.sh │ ├── RunExomiser_case4.sh │ ├── RunExomiser_case5.sh │ ├── RunExomiser_case6.sh │ ├── RunExomiser_case7.sh │ ├── RunExomiser_case8.sh │ └── RunExomiser_case9.sh ├── MakeReadFiles.sh └── igv_snapshot_Variant_Mother_Case5.png ├── LICENSE.txt ├── README.md ├── Resources ├── LoginToWestGrid.md ├── UnixCheatSheet.pdf └── Vidyo_instructions.md ├── Scripts ├── Backup │ ├── BamToSubRegionFastq.sh │ ├── BasicVariables.sh │ ├── DeepVariant_CaseTemplate.sh │ ├── DeepVariant_Proband.sh │ ├── FullPipeline_Case7.sh │ ├── FullPipeline_Sample1.sh │ ├── GATK_HaplotypeCallerPolaris.sh │ ├── InstallPrereqs.sh │ ├── MapAndConvert.sh │ ├── MapAndConvert_Case3.sh │ ├── MapAndConvert_CaseTemplate.sh │ ├── MapAndConvert_ShowingVariables.sh │ ├── PositionSortIndexBams.sh │ ├── RunDeepTrio_CaseTemplate.sh │ ├── RunDeepTrio_Example.sh │ ├── RunExomiser_case4.sh │ ├── Singularity_DeepVariant_Polaris.sh │ ├── SlurmHeader.sh │ └── reference.sh ├── BamToSubRegionFastq.sh ├── BasicVariables.sh ├── Case4_Exomiser.yml ├── DeepVariant_CaseTemplate.sh ├── DeepVariant_Proband.sh ├── FullPipeline_Case7.sh ├── FullPipeline_Sample1.sh ├── GATK_HaplotypeCallerPolaris.sh ├── InstallPrereqs.sh ├── MapAndConvert.sh ├── MapAndConvert_Case3.sh ├── MapAndConvert_CaseTemplate.sh ├── MapAndConvert_ShowingVariables.sh ├── Old │ ├── BothVarCallers_VarCallExome_1kG_NA12889.pbs │ ├── BothVarCallers_VarCallExome_1kG_NA12890.pbs │ ├── ExampleHeader.pbs │ ├── MapAndConvert.pbs │ ├── MapAndConvertExome.pbs │ ├── MapAndConvertExome_NA12889.pbs │ ├── MapAndConvertExome_NA12890.pbs │ ├── MapAndConvertVariables.pbs │ ├── MapAndConvertVariables.sh │ ├── MapAndConvert_Complete.sh │ ├── MapBowtie2Example.pbs │ ├── MapConvertQuantify_ISS_S_2.pbs │ ├── VarCallExome_1kG_NA12889.pbs │ └── VarCallExome_1kG_NA12890.pbs ├── PositionSortIndexBams.sh ├── RunDeepTrio_CaseTemplate.sh ├── RunDeepTrio_Example.sh ├── RunExomiser_case4.sh ├── 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