├── .gitattributes ├── .travis.yml ├── ChangeLog ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── conda ├── build.sh ├── build_config.yaml └── meta.yaml ├── docs ├── Makefile ├── make.bat └── source │ ├── _templates │ ├── navbar.html │ └── sidebartoc.html │ ├── conf.py │ ├── docs │ ├── configuration.rst │ ├── examples.rst │ ├── quickstart.rst │ ├── release_notes.rst │ ├── releases │ │ ├── 0.1-alpha.1.rst │ │ ├── 0.1-alpha.2.rst │ │ ├── 0.1-alpha.3.rst │ │ ├── 0.1-alpha.4.rst │ │ ├── 0.1-alpha.5.rst │ │ ├── 0.1-alpha.6.rst │ │ ├── 0.1-alpha.7.rst │ │ ├── 0.1-beta.1.rst │ │ ├── 0.1-beta.10.rst │ │ ├── 0.1-beta.11.rst │ │ ├── 0.1-beta.2.rst │ │ ├── 0.1-beta.3.rst │ │ ├── 0.1-beta.4.rst │ │ ├── 0.1-beta.5.rst │ │ ├── 0.1-beta.6.rst │ │ ├── 0.1-beta.7.rst │ │ ├── 0.1-beta.8.rst │ │ ├── 0.1-beta.9.rst │ │ ├── 0.1.rst │ │ ├── 0.2.1.rst │ │ ├── 0.2.2.rst │ │ └── 0.2.rst │ ├── resources.rst │ └── troubleshooting.rst │ └── index.rst ├── environment-27.yaml ├── environment-ucsc.yaml ├── environment.yaml ├── requirements.txt ├── scripts ├── deploy.sh ├── syncrules.py ├── travis-setup.sh └── ucsc │ ├── FOOTER │ ├── create-ucsc-rule.py │ └── template.rule ├── setup.cfg ├── setup.py ├── snakemake_rules ├── __init__.py ├── _version.py ├── core │ ├── __init__.py │ ├── ruleinfo.py │ └── utils.py └── rules │ ├── angsd │ ├── angsd.settings.smk │ ├── angsd_domaf.smk │ ├── angsd_dosaf.smk │ ├── angsd_dothetas.smk │ ├── angsd_realsfs.smk │ ├── angsd_thetastat_dostat.smk │ ├── angsd_thetastat_makebed.smk │ └── env.yaml │ ├── annovar │ ├── annovar.settings.smk │ ├── annovar_annotate_variation.smk │ ├── annovar_convert2annovar.smk │ └── annovar_table_annovar.smk │ ├── bamtools │ ├── bamtools.settings.smk │ ├── bamtools_create_filter_script.smk │ ├── bamtools_filter.smk │ ├── bamtools_filter_script.smk │ ├── bamtools_filter_unique.smk │ └── env.yaml │ ├── bcftools │ ├── bcftools.settings.smk │ ├── bcftools_call.smk │ ├── bcftools_call_targets.smk │ ├── bcftools_combine_target_variants.smk │ ├── bcftools_index.smk │ ├── bcftools_isec.smk │ ├── bcftools_isec_AB.smk │ ├── bcftools_stats.smk │ ├── bcftools_view_sample.smk │ └── env.yaml │ ├── bedtools │ ├── bedtools.settings.smk │ ├── bedtools_bamtobed.smk │ ├── bedtools_bedToBedGraph.smk │ ├── bedtools_coverage.smk │ ├── bedtools_intersect.smk │ ├── bedtools_min_genomecov.smk │ └── env.yaml │ ├── blat │ ├── blat.settings.smk │ ├── blat_faToTwoBit.smk │ └── env.yaml │ ├── bowtie │ ├── bowtie.settings.smk │ ├── bowtie_align_pe.smk │ ├── bowtie_build.smk │ └── env.yaml │ ├── bowtie2 │ ├── bowtie2.settings.smk │ ├── bowtie2_align_pe.smk │ ├── bowtie2_align_se.smk │ ├── bowtie2_build.smk │ └── env.yaml │ ├── bwa │ ├── bwa.settings.smk │ ├── bwa_aln.smk │ ├── bwa_aln_samse.smk │ ├── bwa_aln_samse_sort.smk │ ├── bwa_index.smk │ ├── bwa_link_ref.smk │ ├── bwa_mem.smk │ ├── bwa_mem_se.smk │ ├── bwa_samse.smk │ └── env.yaml │ ├── centipede │ └── centipede.settings.smk │ ├── cloudbiolinux │ ├── cloudbiolinux.settings.smk │ └── cloudbiolinux_update_annotation_gtf.smk │ ├── comp │ ├── comp.settings.smk │ ├── settings.smk │ └── utils.smk │ ├── cutadapt │ ├── cutadapt.settings.smk │ ├── cutadapt_cut_fiveprime.smk │ ├── cutadapt_cut_paired_end.smk │ ├── cutadapt_cut_single_end.smk │ ├── cutadapt_cut_threeprime.smk │ ├── cutadapt_save_log.smk │ └── env.yaml │ ├── danpos │ ├── danpos.settings.smk │ ├── danpos_bin_reads_by_nucleosome.smk │ └── danpos_dpos.smk │ ├── dfilter │ ├── dfilter.settings.smk │ └── dfilter_run_dfilter_bam.smk │ ├── diamond │ ├── diamond.settings.smk │ ├── diamond.smk │ └── diamond_blastx.smk │ ├── emacs │ ├── emacs.settings.smk │ └── emacs_org_to_reveal.smk │ ├── emboss │ ├── emboss.settings.smk │ ├── emboss_seqret_fa_to_genbank.smk │ ├── emboss_seqret_fasta_to_genbank.smk │ └── env.yaml │ ├── ercc │ ├── ercc.settings.smk │ ├── ercc_create_ref.smk │ └── ercc_download_metadata.smk │ ├── fastqc │ ├── env.yaml │ ├── fastqc.settings.smk │ └── fastqc.smk │ ├── freebayes │ ├── env.yaml │ ├── freebayes.settings.smk │ ├── freebayes.smk │ ├── freebayes_combine_target_variants.smk │ ├── freebayes_concat_targets.smk │ ├── freebayes_merge_targets.smk │ ├── freebayes_parallel.smk │ └── freebayes_targets.smk │ ├── gatk │ ├── env.yaml │ ├── gatk.settings.smk │ ├── gatk_apply_recalibration.smk │ ├── gatk_base_recalibrator.smk │ ├── gatk_clip_reads.smk │ ├── gatk_combine_gvcfs_targets.smk │ ├── gatk_combine_variants.smk │ ├── gatk_combine_variants_targets.smk │ ├── gatk_combine_variants_windows.smk │ ├── gatk_fasta_alternate_reference_maker.smk │ ├── gatk_genotype_gvcfs.smk │ ├── gatk_haplotype_caller.smk │ ├── gatk_haplotype_caller_combine_target_variants.smk │ ├── gatk_haplotype_caller_targets.smk │ ├── gatk_indel_realigner.smk │ ├── gatk_print_reads.smk │ ├── gatk_read_backed_phasing.smk │ ├── gatk_realigner_target_creator.smk │ ├── gatk_select_indel_variants.smk │ ├── gatk_select_snp_variants.smk │ ├── gatk_select_variants.smk │ ├── gatk_select_variants_region.smk │ ├── gatk_select_variants_sample.smk │ ├── gatk_unified_genotyper.smk │ ├── gatk_variant_JEXL_filtration.smk │ ├── gatk_variant_annotator.smk │ ├── gatk_variant_eval.smk │ ├── gatk_variant_eval_stratify_by_baits.smk │ ├── gatk_variant_indel_JEXL_filtration.smk │ ├── gatk_variant_recalibrator.smk │ ├── gatk_variant_snp_JEXL_filtration.smk │ ├── gatk_variants_to_table.smk │ └── gatk_vqsr_prepare_training_data.smk │ ├── gem │ ├── gem.settings.smk │ ├── gem_indexer.smk │ └── gem_mappability.smk │ ├── homer │ ├── homer.settings.smk │ ├── homer_annotatePeaks.smk │ └── homer_findMotifsGenome.smk │ ├── htslib │ ├── env.yaml │ ├── htslib.settings.smk │ ├── htslib_bgzip.smk │ └── htslib_plot_vcfcheck.smk │ ├── jellyfish │ ├── env.yaml │ ├── jellyfish.settings.smk │ ├── jellyfish_count.smk │ └── jellyfish_histo.smk │ ├── kpal │ ├── env.yaml │ ├── kpal.settings.smk │ ├── kpal_count.smk │ ├── kpal_count_all.smk │ ├── kpal_distance.smk │ └── kpal_matrix.smk │ ├── macs2 │ ├── env.yaml │ ├── macs2.settings.smk │ ├── macs2_callpeak_treatment_only_bam_pe.smk │ └── macs2_xls_to_bed.smk │ ├── main.settings.smk │ ├── malt │ ├── malt.settings.smk │ ├── malt_build.smk │ └── malt_run.smk │ ├── mapdamage2 │ ├── env.yaml │ ├── mapdamage2.settings.smk │ └── mapdamage2.smk │ ├── multiqc │ ├── env.yaml │ ├── multiqc.settings.smk │ └── multiqc.smk │ ├── multo │ └── multo.settings.smk │ ├── ngs.settings.smk │ ├── pandoc │ └── pandoc.settings.smk │ ├── picard │ ├── env.yaml │ ├── picard.settings.smk │ ├── picard_add_or_replace_read_groups.smk │ ├── picard_bed_to_interval_list.smk │ ├── picard_build_bam_index.smk │ ├── picard_calculate_hs_metrics.smk │ ├── picard_calculate_hs_metrics_regions.smk │ ├── picard_collect_alignment_summary_metrics.smk │ ├── picard_collect_insert_size_metrics.smk │ ├── picard_create_sequence_dictionary.smk │ ├── picard_create_sequence_dictionary_awk.smk │ ├── picard_create_sequence_dictionary_region_awk.smk │ ├── picard_do_qc.smk │ ├── picard_interval_list_to_bed.smk │ ├── picard_mark_duplicates.smk │ ├── picard_merge_sam.smk │ ├── picard_reorder_sam.smk │ ├── picard_sequence_dictionary_to_interval_list.smk │ └── picard_sort_sam.smk │ ├── plink │ ├── plink.settings.smk │ ├── plink_bed2ld_r2.smk │ ├── plink_bed2ped.smk │ ├── plink_bed_blocks.smk │ ├── plink_chr_bed.smk │ └── plink_ped2ld_r2.smk │ ├── pybedtools │ ├── env.yaml │ ├── pybedtools.settings.smk │ ├── pybedtools_make_bed_targets.smk │ └── pybedtools_make_bed_windows.smk │ ├── qualimap │ ├── env.yaml │ ├── qualimap.settings.smk │ ├── qualimap_bamqc.smk │ └── qualimap_bamqc_se.smk │ ├── r │ ├── r.settings.smk │ ├── r_rmarkdown.smk │ ├── r_rmarkdown_bookdown.smk │ └── r_rmarkdown_revealjs.smk │ ├── rnaseqc │ └── rnaseqc.settings.smk │ ├── rpkmforgenes │ ├── env.yaml │ ├── rpkmforgenes.settings.smk │ ├── rpkmforgenes_from_bam.smk │ └── rpkmforgenes_from_bed.smk │ ├── rsem │ ├── env.yaml │ ├── rsem.settings.smk │ ├── rsem_calculate_expression.smk │ ├── rsem_calculate_expression_bowtie.smk │ ├── rsem_pca.smk │ ├── rsem_prepare_reference.smk │ └── rsem_remove_soft_clipping.smk │ ├── rseqc │ ├── env.yaml │ ├── rseqc.settings.smk │ ├── rseqc_clipping_profile.smk │ ├── rseqc_geneBody_coverage.smk │ ├── rseqc_junction_annotation.smk │ ├── rseqc_qc.smk │ ├── rseqc_qc_8.smk │ ├── rseqc_read_GC.smk │ ├── rseqc_read_NVC.smk │ ├── rseqc_read_distribution.smk │ ├── rseqc_read_duplication.smk │ └── rseqc_read_quality.smk │ ├── samtools │ ├── env.yaml │ ├── samtools.settings.smk │ ├── samtools_depth.smk │ ├── samtools_faidx.smk │ ├── samtools_gene_region_from_bam.smk │ ├── samtools_index.smk │ ├── samtools_min_depth.smk │ ├── samtools_sam2bam.smk │ ├── samtools_sort.smk │ ├── samtools_stats.smk │ └── samtools_tabix_vcf.smk │ ├── seqtk │ ├── env.yaml │ ├── seqtk.settings.smk │ └── seqtk_seq_fastq_to_fasta.smk │ ├── sga │ ├── sga.settings.smk │ ├── sga_preprocess.smk │ └── sga_preprocess_pe.smk │ ├── snpeff │ ├── env.yaml │ ├── snpeff.settings.smk │ ├── snpeff_annotate_variants.smk │ └── snpeff_download_database.smk │ ├── sratools │ └── sratools.settings.smk │ ├── star │ ├── env.yaml │ ├── star.settings.smk │ ├── star_align_log.smk │ ├── star_align_log_se.smk │ ├── star_align_pe.smk │ ├── star_align_se.smk │ └── star_index.smk │ ├── trim_galore │ └── trim_galore.settings.smk │ ├── trimmomatic │ └── trimmomatic.settings.smk │ ├── tuxedo │ ├── tuxedo.settings.smk │ ├── tuxedo_bowtie2_build.smk │ ├── tuxedo_bowtie_align.smk │ ├── tuxedo_bowtie_build.smk │ ├── tuxedo_cufflinks_from_bam.smk │ ├── tuxedo_cufflinks_from_tophat.smk │ ├── tuxedo_cufflinks_quant.smk │ └── tuxedo_tophat.smk │ ├── ucsc │ ├── envs │ │ ├── ucsc_bedgraphtobigwig.yaml │ │ ├── ucsc_fetchchromsizes.yaml │ │ ├── ucsc_genepredtobed.yaml │ │ ├── ucsc_gtftogenepred.yaml │ │ └── ucsc_wigtobigwig.yaml │ ├── ucsc.settings.smk │ ├── ucsc_bedGraphToBigWig.smk │ ├── ucsc_download_2bit.smk │ ├── ucsc_fetchChromSizes.smk │ ├── ucsc_genePredToBed.smk │ ├── ucsc_genepred_to_refFlat.smk │ ├── ucsc_gtfToGenePred.smk │ ├── ucsc_link.smk │ ├── ucsc_no_alt_analysis_set_reference.smk │ ├── ucsc_pseudo.smk │ ├── ucsc_wigToBigWig.smk │ └── ucsc_write_chromosome.smk │ ├── utils │ ├── conf_yaml.smk │ ├── conversion.smk │ ├── dag.smk │ ├── dag_png.smk │ ├── dbutils_make_transcript_annot_gtf.smk │ ├── gzip.smk │ ├── rulegraph.smk │ ├── rulegraph_png.smk │ └── utils.settings.smk │ ├── vcflib │ ├── env.yaml │ ├── vcfcheck.smk │ └── vcflib.settings.smk │ ├── vcftools │ ├── vcftools.settings.smk │ ├── vcftools_dump_stats.smk │ ├── vcftools_vcf2ped.smk │ ├── vcftools_vcf_freq.smk │ └── vcftools_vcf_freq2.smk │ └── vsearch │ ├── env.yaml │ ├── vsearch.settings.smk │ ├── vsearch_fastq_filter.smk │ └── vsearch_fastq_stats.smk ├── tests ├── config │ ├── config.yaml │ └── sampleinfo.csv ├── conftest.py ├── data │ ├── Snakefile │ ├── bamfiles.fofn │ ├── chrom.sizes │ ├── config.yaml │ ├── dbsnp132_chr11.vcf │ ├── ref-transcripts.bed12 │ ├── ref-transcripts.genePred │ ├── ref-transcripts.gtf │ ├── ref.bed │ ├── ref.dict │ ├── ref.fa │ ├── ref.fa.fai │ ├── ref.interval_list │ ├── s1.revealjs.Rmd │ ├── s1.rg.sort.bai │ ├── s1.rg.sort.bam │ ├── s1.rg.sort.bed │ ├── s1.rg.sort.bedGraph │ ├── s1.rg.sort.bigWig │ ├── s1.rg.sort.g.vcf │ ├── s1.rg.sort.g.vcf.gz │ ├── s1.rg.sort.sam │ ├── s1.rg.sort.vcf │ ├── s1.rg.sort.wig │ ├── s1.vcf.fofn │ ├── s1_1.fastq.gz │ ├── s1_2.fastq.gz │ ├── s2.rg.sort.bai │ ├── s2.rg.sort.bam │ ├── s2.rg.sort.g.vcf │ ├── s2.rg.sort.g.vcf.gz │ ├── s2.rg.sort.vcf │ ├── s2_1.fastq.gz │ ├── s2_2.fastq.gz │ ├── sampleinfo.csv │ ├── targets.bed │ └── targets.interval_list ├── examples │ ├── Snakefile │ ├── Snakefile_regions │ ├── config.yaml │ └── config_regions.yaml ├── helpers │ ├── fixture.py │ ├── inputconfig.yaml │ └── utils.py ├── rules2target.yaml ├── test_core_utils.py ├── test_helpers.py ├── test_ruleinfo.py ├── test_rules.py ├── test_rules_ngsfixtures.py └── test_workflows.py └── versioneer.py 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