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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Name		Name	Last commit message	Last commit date
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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