VaCaPi

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

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
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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