Page Index - genome/analysis-workflows GitHub Wiki

552 page(s) in this GitHub Wiki:

• Home
• Overview
• Featured Pipelines
• Whole Genome Clinical Assay
• Inputs
• Table of Contents
• Tools
• Subworkflows
• Pipelines
• Questions
• Alignment
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• Bisulfite workflow
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• Creating RNAseq annotation files from Ensembl
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• DNA Alignment
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• Frequently Asked Questions (FAQ)
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• Fusions
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• Gathering input files
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• Germline SNVs and small Indels
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• Legacy Setup Instructions
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• Legacy SNVs_and_SmallIndels
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• pipelines
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• pipelines_alignment_exome.cwl
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• pipelines_alignment_exome_nonhuman.cwl
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• pipelines_alignment_umi_duplex.cwl
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• pipelines_alignment_umi_molecular.cwl
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• pipelines_alignment_wgs.cwl
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• pipelines_alignment_wgs_nonhuman.cwl
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• pipelines_aml_trio_cle.cwl
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• pipelines_aml_trio_cle_gathered.cwl
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• pipelines_bisulfite.cwl
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• pipelines_chipseq.cwl
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• pipelines_chipseq_alignment_nonhuman.cwl
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• pipelines_detect_variants.cwl
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• pipelines_detect_variants_nonhuman.cwl
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• pipelines_detect_variants_wgs.cwl
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• pipelines_detect_variants_wgs_nonhuman.cwl
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• pipelines_downsample_and_recall.cwl
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• pipelines_gathered_downsample_and_recall.cwl
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• pipelines_germline_exome.cwl
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• pipelines_germline_exome_gvcf.cwl
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• pipelines_germline_exome_hla_typing.cwl
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• pipelines_germline_wgs.cwl
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• pipelines_germline_wgs_gvcf.cwl
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• pipelines_immuno.cwl
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• pipelines_rnaseq.cwl
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• pipelines_rnaseq_star_fusion.cwl
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• pipelines_rnaseq_star_fusion_with_xenosplit.cwl
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• pipelines_somatic_exome.cwl
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• pipelines_somatic_exome_cle.cwl
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• pipelines_somatic_exome_cle_gathered.cwl
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• pipelines_somatic_exome_gathered.cwl
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• pipelines_somatic_exome_nonhuman.cwl
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• pipelines_somatic_wgs.cwl
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• pipelines_somatic_wgs_nonhuman.cwl
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• pipelines_tumor_only_detect_variants.cwl
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• pipelines_tumor_only_exome.cwl
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• pipelines_tumor_only_wgs.cwl
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• README
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• RnaSeq
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• Single Sample SVs
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• subworkflows
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• subworkflows_align.cwl
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• subworkflows_align_sort_markdup.cwl
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• subworkflows_bam_readcount.cwl
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• subworkflows_bam_to_trimmed_fastq_and_biscuit_alignments.cwl
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• subworkflows_bgzip_and_index.cwl
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• subworkflows_bisulfite_qc.cwl
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• subworkflows_cellranger_mkfastq_and_count.cwl
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• subworkflows_cnvkit_single_sample.cwl
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• subworkflows_cram_to_bam_and_index.cwl
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• subworkflows_cram_to_cnvkit.cwl
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• subworkflows_docm_cle.cwl
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• subworkflows_docm_germline.cwl
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• subworkflows_duplex_alignment.cwl
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• subworkflows_filter_vcf.cwl
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• subworkflows_filter_vcf_nonhuman.cwl
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• subworkflows_fp_filter.cwl
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• subworkflows_gatk_haplotypecaller_iterator.cwl
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• subworkflows_generate_fda_metrics.cwl
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• subworkflows_germline_detect_variants.cwl
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• subworkflows_germline_filter_vcf.cwl
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• subworkflows_hs_metrics.cwl
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• subworkflows_joint_genotype.cwl
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• subworkflows_merge_svs.cwl
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• subworkflows_molecular_alignment.cwl
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• subworkflows_molecular_qc.cwl
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• subworkflows_mutect.cwl
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• subworkflows_phase_vcf.cwl
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• subworkflows_pindel.cwl
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• subworkflows_pindel_cat.cwl
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• subworkflows_pindel_region.cwl
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• subworkflows_pvacseq.cwl
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• subworkflows_qc_exome.cwl
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• subworkflows_qc_exome_no_verify_bam.cwl
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• subworkflows_qc_wgs.cwl
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• subworkflows_qc_wgs_nonhuman.cwl
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• subworkflows_sequence_align_and_tag_adapter.cwl
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• subworkflows_sequence_to_bqsr.cwl
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• subworkflows_sequence_to_bqsr_nonhuman.cwl
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• subworkflows_sequence_to_trimmed_fastq.cwl
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• subworkflows_sequence_to_trimmed_fastq_and_hisat_alignments.cwl
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• subworkflows_single_cell_rnaseq.cwl
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• subworkflows_single_sample_sv_callers.cwl
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• subworkflows_strelka_and_post_processing.cwl
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• subworkflows_strelka_process_vcf.cwl
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• subworkflows_sv_depth_caller_filter.cwl
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• subworkflows_sv_paired_read_caller_filter.cwl
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• subworkflows_umi_alignment.cwl
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• subworkflows_varscan.cwl
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• subworkflows_varscan_germline.cwl
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• subworkflows_varscan_pre_and_post_processing.cwl
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• subworkflows_vcf_eval_cle_gold.cwl
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• subworkflows_vcf_eval_concordance.cwl
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• subworkflows_vcf_readcount_annotator.cwl
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• tools
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• tools_add_strelka_gt.cwl
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• tools_add_string_at_line.cwl
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• tools_add_string_at_line_bgzipped.cwl
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• tools_add_vep_fields_to_table.cwl
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• tools_agfusion.cwl
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• tools_align_and_tag.cwl
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• tools_aligned_seq_fda_stats.cwl
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• tools_annotsv.cwl
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• tools_annotsv_filter.cwl
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• tools_apply_bqsr.cwl
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• tools_bam_readcount.cwl
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• tools_bam_to_bigwig.cwl
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• tools_bam_to_cram.cwl
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• tools_bam_to_fastq.cwl
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• tools_bam_to_sam.cwl
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• tools_bcftools_merge.cwl
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• tools_bedgraph_to_bigwig.cwl
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• tools_bedtools_intersect.cwl
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• tools_bgzip.cwl
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• tools_biscuit_align.cwl
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• tools_biscuit_markdup.cwl
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• tools_biscuit_pileup.cwl
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• tools_bisulfite_qc_conversion.cwl
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• tools_bisulfite_qc_coverage_stats.cwl
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• tools_bisulfite_qc_cpg_retention_distribution.cwl
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• tools_bisulfite_qc_mapping_summary.cwl
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• tools_bisulfite_vcf2bed.cwl
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• tools_bqsr.cwl
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• tools_call_duplex_consensus.cwl
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• tools_call_molecular_consensus.cwl
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• tools_cat_all.cwl
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• tools_cat_out.cwl
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• tools_cellmatch_lineage.cwl
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• tools_cellranger_atac_count.cwl
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• tools_cellranger_count.cwl
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• tools_cellranger_feature_barcoding.cwl
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• tools_cellranger_mkfastq.cwl
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• tools_cellranger_vdj.cwl
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• tools_cle_aml_trio_report_alignment_stat.cwl
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• tools_cle_aml_trio_report_coverage_stat.cwl
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• tools_cle_aml_trio_report_full_variants.cwl
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• tools_clip_overlap.cwl
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• tools_cnvkit_batch.cwl
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• tools_cnvkit_vcf_export.cwl
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• tools_cnvnator.cwl
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• tools_collect_alignment_summary_metrics.cwl
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• tools_collect_gc_bias_metrics.cwl
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• tools_collect_hs_metrics.cwl
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• tools_collect_insert_size_metrics.cwl
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• tools_collect_wgs_metrics.cwl
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• tools_combine_gvcfs.cwl
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• tools_combine_variants.cwl
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• tools_combine_variants_concordance.cwl
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• tools_combine_variants_wgs.cwl
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• tools_concordance.cwl
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• tools_cram_to_bam.cwl
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• tools_docm_add_variants.cwl
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• tools_docm_gatk_haplotype_caller.cwl
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• tools_downsample.cwl
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• tools_duphold.cwl
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• tools_duplex_seq_metrics.cwl
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• tools_eval_cle_gold.cwl
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• tools_eval_vaf_report.cwl
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• tools_extract_hla_alleles.cwl
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• tools_extract_umis.cwl
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• tools_fastq_to_bam.cwl
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• tools_fastqc.cwl
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• tools_filter_consensus.cwl
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• tools_filter_known_variants.cwl
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• tools_filter_sv_vcf_blocklist_bedpe.cwl
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• tools_filter_sv_vcf_depth.cwl
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• tools_filter_sv_vcf_read_support.cwl
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• tools_filter_sv_vcf_size.cwl
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• tools_filter_vcf_cle.cwl
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• tools_filter_vcf_coding_variant.cwl
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• tools_filter_vcf_custom_allele_freq.cwl
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• tools_filter_vcf_depth.cwl
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• tools_filter_vcf_docm.cwl
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• tools_filter_vcf_mapq0.cwl
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• tools_filter_vcf_somatic_llr.cwl
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• tools_fix_vcf_header.cwl
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• tools_fp_filter.cwl
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• tools_gather_to_sub_directory.cwl
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• tools_gatherer.cwl
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• tools_gatk_genotypegvcfs.cwl
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• tools_gatk_haplotype_caller.cwl
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• tools_generate_fda_tables.cwl
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• tools_generate_qc_metrics.cwl
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• tools_germline_combine_variants.cwl
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• tools_grolar.cwl
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• tools_group_reads.cwl
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• tools_hisat2_align.cwl
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• tools_hla_consensus.cwl
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• tools_homer_tag_directory.cwl
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• tools_index_bam.cwl
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• tools_index_cram.cwl
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• tools_index_vcf.cwl
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• tools_intersect_known_variants.cwl
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• tools_interval_list_expand.cwl
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• tools_intervals_to_bed.cwl
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• tools_kallisto.cwl
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• tools_kmer_size_from_index.cwl
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• tools_manta_somatic.cwl
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• tools_mark_duplicates_and_sort.cwl
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• tools_mark_illumina_adapters.cwl
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• tools_md5sum.cwl
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• tools_merge_bams.cwl
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• tools_merge_bams_samtools.cwl
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• tools_merge_vcf.cwl
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• tools_mutect.cwl
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• tools_name_sort.cwl
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• tools_normalize_variants.cwl
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• tools_optitype_dna.cwl
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• tools_picard_merge_vcfs.cwl
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• tools_pindel.cwl
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• tools_pindel2vcf.cwl
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• tools_pindel_somatic_filter.cwl
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• tools_pizzly.cwl
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• tools_pvacbind.cwl
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• tools_pvacfuse.cwl
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• tools_pvacseq.cwl
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• tools_pvacseq_combine_variants.cwl
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• tools_pvacvector.cwl
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• tools_read_backed_phasing.cwl
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• tools_realign.cwl
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• tools_remove_end_tags.cwl
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• tools_rename.cwl
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• tools_rename_for_staging.cwl
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• tools_replace_vcf_sample_name.cwl
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• tools_samtools_flagstat.cwl
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• tools_samtools_sort.cwl
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• tools_select_variants.cwl
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• tools_sequence_align_and_tag.cwl
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• tools_sequence_to_bam.cwl
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• tools_sequence_to_fastq.cwl
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• tools_set_filter_status.cwl
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• tools_single_sample_docm_filter.cwl
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• tools_smoove.cwl
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• tools_somatic_concordance_graph.cwl
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• tools_sompy.cwl
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• tools_sort_vcf.cwl
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• tools_split_interval_list.cwl
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• tools_split_interval_list_to_bed.cwl
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• tools_staged_rename.cwl
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• tools_star_align_fusion.cwl
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• tools_star_fusion_detect.cwl
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• tools_strandedness_check.cwl
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• tools_strelka.cwl
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• tools_stringtie.cwl
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• tools_survivor.cwl
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• tools_transcript_to_gene.cwl
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• tools_trim_fastq.cwl
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• tools_umi_align.cwl
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• tools_unaligned_seq_fda_stats.cwl
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• tools_variants_to_table.cwl
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• tools_varscan_germline.cwl
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• tools_varscan_process_somatic.cwl
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• tools_varscan_somatic.cwl
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• tools_vcf_expression_annotator.cwl
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• tools_vcf_readcount_annotator.cwl
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• tools_vcf_sanitize.cwl
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• tools_vep.cwl
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• tools_verify_bam_id.cwl
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• tools_vt_decompose.cwl
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• tools_xenosplit.cwl
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• Whole Genome Sequencing Clinical Assay
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