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LICENSE
LICENSE
 
 
NGS_ANALYSIS_MedGen.sh
NGS_ANALYSIS_MedGen.sh
 
 
NGS_ANALYSIS_MedGen_02.03.2016.sh
NGS_ANALYSIS_MedGen_02.03.2016.sh
 
 
NGS_ANALYSIS_MedGen_06.01.2016.sh
NGS_ANALYSIS_MedGen_06.01.2016.sh
 
 
NGS_ANALYSIS_MedGen_18.07.2016.sh
NGS_ANALYSIS_MedGen_18.07.2016.sh
 
 
NGS_ANALYSIS_MedGen_24.05.2016.sh
NGS_ANALYSIS_MedGen_24.05.2016.sh
 
 
NGS_ANALYSIS_MedGen_27.06.2016.sh
NGS_ANALYSIS_MedGen_27.06.2016.sh
 
 
NGS_ANALYSIS_MedGen_30.11.2016.sh
NGS_ANALYSIS_MedGen_30.11.2016.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL.sh
NGS_ANALYSIS_MedGen_NEW_PANEL.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_01_05_2017.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_01_05_2017.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_07_08_2017.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_07_08_2017.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_03_01_2018.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_03_01_2018.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_with_static_pooling.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_with_static_pooling.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_with_static_pooling_21_06_2018.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_analysis_included_with_static_pooling_21_06_2018.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_test_run_11_09_2017.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_CNV_test_run_11_09_2017.sh
 
 
NGS_ANALYSIS_MedGen_NEW_PANEL_latest_backup.sh
NGS_ANALYSIS_MedGen_NEW_PANEL_latest_backup.sh
 
 
NGS_ANALYSIS_MedGen_latest_backup.sh
NGS_ANALYSIS_MedGen_latest_backup.sh
 
 
NGS_ANALYSIS_MedGen_with_gender_control.sh
NGS_ANALYSIS_MedGen_with_gender_control.sh
 
 
NGS_Analysis_parallel_DYNAMIC_QC.sh
NGS_Analysis_parallel_DYNAMIC_QC.sh
 
 
NGS_Analysis_parallel_DYNAMIC_sample.sh
NGS_Analysis_parallel_DYNAMIC_sample.sh
 
 
NGS_Analysis_parallel_v3.1.sh
NGS_Analysis_parallel_v3.1.sh
 
 
NGS_dynamic_backup_code.sh
NGS_dynamic_backup_code.sh
 
 
NexteraRapidCapture-112662-FINAL-targeted-regions_V1.bed
NexteraRapidCapture-112662-FINAL-targeted-regions_V1.bed
 
 
NexteraRapidCapture-71370-targeted-regions_v4.bed
NexteraRapidCapture-71370-targeted-regions_v4.bed
 
 
Pipeline_version.txt
Pipeline_version.txt
 
 
README.md
README.md
 
 
R_code_for_gap_region_generation.r
R_code_for_gap_region_generation.r
 
 
R_code_for_gap_region_generation_18.07.2016.r
R_code_for_gap_region_generation_18.07.2016.r
 
 
Steps_NGS_analsysis_v3.sh
Steps_NGS_analsysis_v3.sh
 
 
Target_Nucleotide_annotated_NEW.csv
Target_Nucleotide_annotated_NEW.csv
 
 
Target_ex_n_gn_mdfd_strtPlus1_merged_regions_for_CovRept_2120.bed
Target_ex_n_gn_mdfd_strtPlus1_merged_regions_for_CovRept_2120.bed
 
 
Target_ex_n_gn_mdfd_strtPlus1_merged_regions_for_CovRept_2216_NEW.bed
Target_ex_n_gn_mdfd_strtPlus1_merged_regions_for_CovRept_2216_NEW.bed
 
 
Target_with_exon_and_gene_info.bed
Target_with_exon_and_gene_info.bed
 
 
Target_with_gene_info_NEW.bed
Target_with_gene_info_NEW.bed
 
 
Variant_annotation_ANNOVAR.sh
Variant_annotation_ANNOVAR.sh
 
 
access-10kb.mn10.bed
access-10kb.mn10.bed
 
 
code_for_CNV_analysis.sh
code_for_CNV_analysis.sh
 
 
code_for_mapping_summary.sh
code_for_mapping_summary.sh
 
 
code_low_MQ_analysis.sh
code_low_MQ_analysis.sh
 
 
code_to_pick_selective_genes.sh
code_to_pick_selective_genes.sh
 
 
coverage_analysis.sh
coverage_analysis.sh
 
 
flag_property
flag_property
 
 
mapping_statistics.sh
mapping_statistics.sh
 
 
pipeline_modifications_log
pipeline_modifications_log
 
 
vacapi.sh
vacapi.sh
 
 

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VaCaPi

GATK guideline based Varient calling pipeline Focused on panel based miSEQ data. filtering setting are based on small size of selective genes

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GATK guideline based Varient calling pipeline

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