Create snakeATAC_analyses_config.yaml

config/snakeATAC_analyses_config.yaml

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+# This .yaml cofinguration file contains all variables used by the snakemake pipeline
+# DO NOT CHANGE parameter names without changing it in Snakefile as well
+# On the other hand, some parameter values have to be inevitably modifed
+# **********************************************************************************************************************************
+
+### 1. General workflow parameters  --------------------------------------------------------------------------------------------------
+workflow_configuration:
+  runs_directory: "/path/to/your/bam_directory"
+  output_directory: "/path/to/output/folder"
+
+bam_features:
+  bam_suffix: "_mapq20_sorted_woMT_dedup.bam"
+  skip_bam_filtering: True
+  umi_present: False
+  remove_duplicates: True
+  MAPQ_threshold: 20
+  minFragmentLength: 0
+  maxFragmentLength: 2000
+
+genomic_annotations:
+  genome_id: "hg38"
+  genome_fasta: "/path/to/hg38_genome.fa"
+  blacklist: "/home/user/blacklist/hg38-blacklist.v2.bed"
+  effective_genomeSize: 2900338458
+  ignore_for_normalization: "X Y MT M KI270728.1 KI270727.1 KI270442.1 KI270729.1 GL000225.1 KI270743.1 GL000008.2 GL000009.2 KI270747.1 KI270722.1 GL000194.1 KI270742.1 GL000205.2 GL000195.1 KI270736.1 KI270733.1 GL000224.1 GL000219.1 KI270719.1 GL000216.2 KI270712.1 KI270706.1 KI270725.1 KI270744.1 KI270734.1 GL000213.1 GL000220.1 KI270715.1 GL000218.1 KI270749.1 KI270741.1 GL000221.1 KI270716.1 KI270731.1 KI270751.1 KI270750.1 KI270519.1 GL000214.1 KI270708.1 KI270730.1 KI270438.1 KI270737.1 KI270721.1 KI270738.1 KI270748.1 KI270435.1 GL000208.1 KI270538.1 KI270756.1 KI270739.1 KI270757.1 KI270709.1 KI270746.1 KI270753.1 KI270589.1 KI270726.1 KI270735.1 KI270711.1 KI270745.1 KI270714.1 KI270732.1 KI270713.1 KI270754.1 KI270710.1 KI270717.1 KI270724.1 KI270720.1 KI270723.1 KI270718.1 KI270317.1 KI270740.1 KI270755.1 KI270707.1 KI270579.1 KI270752.1 KI270512.1 KI270322.1 GL000226.1 KI270311.1 KI270366.1 KI270511.1 KI270448.1 KI270521.1 KI270581.1 KI270582.1 KI270515.1 KI270588.1 KI270591.1 KI270522.1 KI270507.1 KI270590.1 KI270584.1 KI270320.1 KI270382.1 KI270468.1 KI270467.1 KI270362.1 KI270517.1 KI270593.1 KI270528.1 KI270587.1 KI270364.1 KI270371.1 KI270333.1 KI270374.1 KI270411.1 KI270414.1 KI270510.1 KI270390.1 KI270375.1 KI270420.1 KI270509.1 KI270315.1 KI270302.1 KI270518.1 KI270530.1 KI270304.1 KI270418.1 KI270424.1 KI270417.1 KI270508.1 KI270303.1 KI270381.1 KI270529.1 KI270425.1 KI270396.1 KI270363.1 KI270386.1 KI270465.1 KI270383.1 KI270384.1 KI270330.1 KI270372.1 KI270548.1 KI270580.1 KI270387.1 KI270391.1 KI270305.1 KI270373.1 KI270422.1 KI270316.1 KI270338.1 KI270340.1 KI270583.1 KI270334.1 KI270429.1 KI270393.1 KI270516.1 KI270389.1 KI270466.1 KI270388.1 KI270544.1 KI270310.1 KI270412.1 KI270395.1 KI270376.1 KI270337.1 KI270335.1 KI270378.1 KI270379.1 KI270329.1 KI270419.1 KI270336.1 KI270312.1 KI270539.1 KI270385.1 KI270423.1 KI270392.1 KI270394.1"
+
+
+
+### 2. MACS3 peak calling ------------------------------------------------------------------------------------------------------------
+peak_calling:
+  qValue_cutoff: 0.001
+  call_summits: True
+  FRiP_threshold: 20 #%
+  peak_score_heatmap:
+    plot_heatmap: False
+    raw_heatmap_color: "Blues"
+    zScore_heatmap_color: "seismic"
+
+
+
+## 3. Quality controls ---------------------------------------------------------------------------------------------------------------
+quality_controls:
+  fragmentSize_window_length: 1000 #bp
+  multiBigwigSummary_binning_window_size: 10000 #bp
+  correlation_heatmap_color: "Blues"
+  plotFingerprint:
+    binSize: 500 #bp
+    sampledRegions: 500000
+    extra_parameters: ""
+
+
+
+### 4. Somatic Variants --------------------------------------------------------------------------------------------------------------
+somatic_variants:
+  call_SNPs: False
+  call_indels: False
+  dbsnp_file: "/path/to/dbsnp_file.vcf.gz"    # To make dbSNP without 'chr' -->  awk '{gsub(/\chr/, "")}1' your.vcf > withoutchr.vcf
+  DP_snp_threshold: 20
+  QUAL_snp_threshold: 0
+  DP_indel_threshold: 20
+  QUAL_indel_threshold: 0
+  SnpSift_vcf_fields_to_extract: [ "CHROM", "POS", "ID", "REF", "ALT", "QUAL", "DP", "AF", "FILTER", "FORMAT", "GEN[*].GT", "GEN[*].AD", "GEN[*].AF" ]
+
+
+
+### 6. Copy Number Variations ---------------------------------------------------------------------------------------------------------
+copy_number_variation:
+  call_CNV: False
+  kb_bin_resolution: 20
+  CNA_threshold: 2
+  CNA_plot_line_colors: "red"  # any R-supported
+  CNA_plot_point_size: 0.5
+  CNA_plot_point_transparency: 0.5
+  corrected_bigWig_binSize: 10 #bp