GitHub - AshKernow/Deprecated_exome-vc-pipeline: Exome variant calling pipeline using BWA mem, Stampy, GATK plus samtools etc.

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Exome variant calling pipeline using BWA mem, Stampy, GATK plus samtools etc.

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Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
ExmAdHoc.1.ReorderSBam.sh		ExmAdHoc.1.ReorderSBam.sh
ExmAdHoc.2.GetQualityMetricsSBam.sh		ExmAdHoc.2.GetQualityMetricsSBam.sh
ExmAdHoc.3.SplitBamtoCHR.sh		ExmAdHoc.3.SplitBamtoCHR.sh
ExmAln.1.Start_Exome_Analysis_Pipeline.sh		ExmAln.1.Start_Exome_Analysis_Pipeline.sh
ExmAln.1b.Start_Realign_and_recalibrate_BAMS.sh		ExmAln.1b.Start_Realign_and_recalibrate_BAMS.sh
ExmAln.2.Align_BWA.sh		ExmAln.2.Align_BWA.sh
ExmAln.3.ConvSamtoBam.sh		ExmAln.3.ConvSamtoBam.sh
ExmAln.4.LocalRealignment.sh		ExmAln.4.LocalRealignment.sh
ExmAln.4a.GC_metrics.sh		ExmAln.4a.GC_metrics.sh
ExmAln.5.GenerateBQSRTable.sh		ExmAln.5.GenerateBQSRTable.sh
ExmAln.6.ApplyRecalibration.sh		ExmAln.6.ApplyRecalibration.sh
ExmAln.6a.AnalyseCovariation.sh		ExmAln.6a.AnalyseCovariation.sh
ExmAln.7.ReduceReads.sh		ExmAln.7.ReduceReads.sh
ExmAln.8a.DepthofCoverage.sh		ExmAln.8a.DepthofCoverage.sh
ExmAln.TEST.AlignSTAMPY.sh		ExmAln.TEST.AlignSTAMPY.sh
ExmAln.TEST.ConvSamtoBam.sh		ExmAln.TEST.ConvSamtoBam.sh
ExmAln.TEST.ConvSamtoBamandDedup.sh		ExmAln.TEST.ConvSamtoBamandDedup.sh
ExmQC.1.Run_FastQC_on_File_List.sh		ExmQC.1.Run_FastQC_on_File_List.sh
ExmRes.1.MakeExomeCaptureTargetBedFile.R		ExmRes.1.MakeExomeCaptureTargetBedFile.R
ExmRes.2.bwa_index_reference.sh		ExmRes.2.bwa_index_reference.sh
ExmRes.3.Stampy_build_reference.sh		ExmRes.3.Stampy_build_reference.sh
ExmRes.4.ANNOVAR_download_databases.sh		ExmRes.4.ANNOVAR_download_databases.sh
ExmVC.1.Start_Exome_Variant_Calling.sh		ExmVC.1.Start_Exome_Variant_Calling.sh
ExmVC.2hc.HaplotypeCaller.sh		ExmVC.2hc.HaplotypeCaller.sh
ExmVC.2ug.UnifiedGenotyper.sh		ExmVC.2ug.UnifiedGenotyper.sh
ExmVC.3.MergeVCF.sh		ExmVC.3.MergeVCF.sh
ExmVC.4.RecalibrateVariantQuality.sh		ExmVC.4.RecalibrateVariantQuality.sh
ExmVC.5.AnnotatewithANNOVAR.sh		ExmVC.5.AnnotatewithANNOVAR.sh
ExmVC.6R.BuildVCF.R		ExmVC.6R.BuildVCF.R
Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V4_b37.sh		Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V4_b37.sh
Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V4_hg19.sh		Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V4_hg19.sh
Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V5_b37.sh		Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V5_b37.sh
Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V5_hg19.sh		Exome_pipeline_settings_Agilent_SureSelect_All_Exon_V5_hg19.sh
Exome_pipeline_settings_unknownTarget_hg19.sh		Exome_pipeline_settings_unknownTarget_hg19.sh
README		README
VCF_header_INFO_for_ANNOVAR.txt		VCF_header_INFO_for_ANNOVAR.txt

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BISR Exome Analysis Pipeline 2013-2014
The pipeline is for initial analysis of Exome Sequencing data from raw sequence reads as fastq files to variant calling.