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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,3 @@ | ||
| sample tumor_content sex | ||
| NA12878 1.0 O | ||
| NA12878 1.0 K | ||
| HD829 1.0 O |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,47 @@ | ||
| decimalPoint_format: ',' | ||
| extra_fn_clean_exts: ##from this until end | ||
| - '.duplication_metrics' | ||
| - type: regex | ||
| pattern: '^HG[0-9]+-[A-Za-z0-9-]+_' | ||
| - type: regex | ||
| pattern: '_fastq[12]' | ||
| extra_fn_clean_trim: | ||
| - 'Sample_WA-3560_' | ||
|
|
||
| table_sample_merge: | ||
| "R1": "_R1_001" | ||
| "R2": "_R2_001" | ||
| "L008": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L008" | ||
| "L007": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L007" | ||
| "L006": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L006" | ||
| "L005": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_[0-9]{1,2}_L005" | ||
| "L004": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L004" | ||
| "L003": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L003" | ||
| "L002": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L002" | ||
| "L001": # to remove SX_L00X from ending to enable grouping | ||
| - type: "regex" | ||
| pattern: "_S[0-9]{1,2}_L001" | ||
|
|
||
| report_header_info: | ||
| - Contact E-mail: "[email protected]" | ||
| - Application Type: "TrueSeq PCR Free WGS" | ||
| - Project Type: "Whole Genome" | ||
|
|
||
| custom content: | ||
| order: | ||
| - fastqc | ||
| - mosdepth | ||
| - fastp | ||
| - peddy | ||
| - samtools | ||
| - picard | ||
|
|
||
| sp: | ||
| dna_number_table: | ||
| fn: "*DNA_number.table.tsv" | ||
|
|
||
| custom_data: | ||
| dna_number_table: | ||
|
|
@@ -32,11 +54,45 @@ custom_data: | |
| title: "DNA number" | ||
| description: "DNA number based on SampleSheet" | ||
|
|
||
| sp: | ||
| dna_number_table: | ||
| fn: "*DNA_number.table.tsv" | ||
| # mosdepth custom thresholds | ||
| mosdepth_config: | ||
| general_stats_coverage: | ||
| - 1 | ||
| - 5 | ||
| - 10 | ||
| - 15 | ||
| - 20 | ||
| - 30 | ||
| - 50 | ||
|
|
||
| # Remove suffix in general stats | ||
| custom_table_header_config: | ||
| general_stats_table: | ||
| raw_total_sequences: | ||
| suffix: "" | ||
| title: "Total seqs [M]" | ||
| reads_mapped: | ||
| suffix: "" | ||
| title: "Reads mapped [M]" | ||
| reads_mapped_percent: | ||
| suffix: "" | ||
| reads_properly_paired_percent: | ||
| suffix: "" | ||
| median_coverage: | ||
| suffix: "" | ||
| 10_x_pc: | ||
| suffix: "" | ||
| 30_x_pc: | ||
| suffix: "" | ||
| 50_x_pc: | ||
| suffix: "" | ||
| PERCENT_DUPLICATION: | ||
| suffix: "" | ||
| title: "Duplication [%]" | ||
| summed_mean: | ||
| suffix: "" | ||
|
|
||
| # General stats column visibility | ||
| table_columns_visible: | ||
| FastQC: | ||
| percent_duplicates: False | ||
|
|
@@ -45,7 +101,7 @@ table_columns_visible: | |
| percent_fails: False | ||
| total_sequences: False | ||
| fastp: | ||
| pct_adapter: True | ||
| pct_adapter: False | ||
| pct_surviving: False | ||
| after_filtering_gc_content: False | ||
| filtering_result_passed_filter_reads: False | ||
|
|
@@ -68,41 +124,33 @@ table_columns_visible: | |
| sex_het_ratio: False | ||
| error_sex_check: True | ||
| predicted_sex_sex_check: True | ||
| Picard: | ||
| PCT_PF_READS_ALIGNED: False | ||
| "Picard: HsMetrics": | ||
| FOLD_ENRICHMENT: False | ||
| MEDIAN_TARGET_COVERAGE: False | ||
| PCT_TARGET_BASES_30X: False | ||
| ZERO_CVG_TARGETS_PCT: False | ||
| "Picard: InsertSizeMetrics": | ||
| summed_median: False | ||
| summed_mean: True | ||
| "Picard: Mark Duplicates": | ||
| PERCENT_DUPLICATION: True | ||
| "Picard: WgsMetrics": | ||
| MEDIAN_COVERAGE: False | ||
| MEAN_COVERAGE: False | ||
| SD_COVERAGE: False | ||
| PCT_30X: False | ||
| PCT_TARGET_BASES_30X: False | ||
| FOLD_ENRICHMENT: False | ||
| TOTAL_READS: True | ||
| Samtools: | ||
| "Samtools: stats": | ||
| error_rate: False | ||
| non-primary_alignments: False | ||
| reads_mapped: False | ||
| reads_mapped_percent: True | ||
| reads_properly_paired_percent: True | ||
| reads_MQ0_percent: False | ||
| raw_total_sequences: True | ||
|
|
||
| # mosdepth custom thresholds | ||
| mosdepth_config: | ||
| general_stats_coverage: | ||
| - 1 | ||
| - 5 | ||
| - 10 | ||
| - 15 | ||
| - 20 | ||
| - 30 | ||
| - 50 | ||
| raw_total_sequences: True #tidigare from picard | ||
|
|
||
| # Patriks plug in, addera egna columner till general stats | ||
| # Custom columns to general stats | ||
| multiqc_cgs: | ||
| Picard: | ||
| "Picard: HsMetrics": | ||
| FOLD_80_BASE_PENALTY: | ||
| title: "Fold80" | ||
| description: "Fold80 penalty from picard hs metrics" | ||
|
|
@@ -121,25 +169,17 @@ multiqc_cgs: | |
| max: 100 | ||
| scale: "RdYlGn-rev" | ||
| format: "{:.2%}" | ||
| Samtools: | ||
| "Samtools: stats": | ||
| average_quality: | ||
| title: "Average Quality" | ||
| description: "Ratio between the sum of base qualities and total length from Samtools stats" | ||
| min: 0 | ||
| max: 60 | ||
| scale: "RdYlGn" | ||
| mosdepth: | ||
| 20_x_pc: #Cant get it to work | ||
| title: "20x percent" | ||
| description: "Fraction of genome with at least 20X coverage" | ||
| max: 100 | ||
| min: 0 | ||
| suffix: "%" | ||
| scale: "RdYlGn" | ||
|
|
||
| # Galler alla kolumner oberoende pa module! | ||
| table_columns_placement: | ||
| dna_number_table: | ||
| "Custom content: dna_number_table": | ||
| dna_number: 300 | ||
| mosdepth: | ||
| median_coverage: 601 | ||
|
|
@@ -150,7 +190,7 @@ table_columns_placement: | |
| 20_x_pc: 604 | ||
| 30_x_pc: 605 | ||
| 50_x_pc: 606 | ||
| Samtools: | ||
| "Samtools: stats": | ||
| raw_total_sequences: 500 | ||
| reads_mapped: 501 | ||
| reads_mapped_percent: 502 | ||
|
|
@@ -166,19 +206,15 @@ table_columns_placement: | |
| error_sex_check: 701 | ||
| predicted_sex_sex_check: 702 | ||
| family_id: 703 | ||
| Picard: | ||
| TOTAL_READS: 500 | ||
| PCT_SELECTED_BASES: 801 | ||
| FOLD_80_BASE_PENALTY: 802 | ||
| PCT_PF_READS_ALIGNED: 888 | ||
| summed_median: 888 | ||
| PERCENT_DUPLICATION: 803 | ||
| summed_mean: 804 | ||
| STANDARD_DEVIATION: 805 | ||
| ZERO_CVG_TARGETS_PCT: 888 | ||
| MEDIAN_COVERAGE: 888 | ||
| MEAN_COVERAGE: 888 | ||
| SD_COVERAGE: 888 | ||
| PCT_30X: 888 | ||
| PCT_TARGET_BASES_30X: 888 | ||
| "Picard: HsMetrics": | ||
| FOLD_ENRICHMENT: 888 | ||
| MEDIAN_TARGET_COVERAGE: 888 | ||
| PCT_TARGET_BASES_30X: 888 | ||
| FOLD_80_BASE_PENALTY: 801 | ||
| PCT_SELECTED_BASES: 800 | ||
| ZERO_CVG_TARGETS_PCT: 805 | ||
| "Picard: InsertSizeMetrics": | ||
| summed_median: 803 | ||
| summed_mean: 803 | ||
| "Picard: Mark Duplicates": | ||
| PERCENT_DUPLICATION: 802 | ||
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