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Files Supported

Source: vignettes/files.Rmd
files.Rmd

Below are the files output from UMCCR workflows that are supported by {dracarys}.

Workflows

N file description
1 replay.json NA
2 fastqc_metrics.csv NA
3 fragment_length_hist.csv NA
4 mapping_metrics.csv NA
5 ploidy_estimation_metrics.csv NA
6 time_metrics.csv NA
7 trimmer_metrics.csv NA
8 wgs_contig_mean_cov.csv NA
9 wgs_coverage_metrics.csv NA
10 wgs_fine_hist.csv NA
11 wgs_hist.csv NA
N file description
1 replay.json NA
2 fastqc_metrics.csv NA
3 fragment_length_hist.csv NA
4 mapping_metrics.csv NA
5 ploidy_estimation_metrics.csv NA
6 time_metrics.csv NA
7 trimmer_metrics.csv NA
8 wgs_contig_mean_cov.csv NA
9 wgs_coverage_metrics.csv NA
10 wgs_fine_hist.csv NA
11 wgs_hist.csv NA
12 fusion_metrics.csv TODO
13 quant_metrics.csv TODO: QC for RNA txs and quantification
14 quant.transcript_fragment_lengths.txt TODO: Full fragment length distribution of reads mapped to txs
15 quant.transcript_coverage.txt TODO: Coverage uniformity with avg of 5’ to 3’ cvg pattern along txs
16 saturation.txt TODO: sequencing saturation, num of unique splice junctions observed
N file description
1 replay.json NA
2 fastqc_metrics.csv NA
3 fragment_length_hist.csv NA
4 mapping_metrics.csv NA
5 ploidy_estimation_metrics.csv NA
6 time_metrics.csv NA
7 trimmer_metrics.csv NA
8 wgs_contig_mean_cov.csv NA
9 wgs_coverage_metrics.csv NA
10 wgs_fine_hist.csv NA
11 wgs_hist.csv NA
12 fusion_metrics.csv TODO
13 quant_metrics.csv TODO: QC for RNA txs and quantification
14 quant.transcript_fragment_lengths.txt TODO: Full fragment length distribution of reads mapped to txs
15 quant.transcript_coverage.txt TODO: Coverage uniformity with avg of 5’ to 3’ cvg pattern along txs
16 saturation.txt TODO: sequencing saturation, num of unique splice junctions observed
N file description
1 replay.json NA
2 fastqc_metrics.csv NA
3 fragment_length_hist.csv NA
4 mapping_metrics.csv NA
5 ploidy_estimation_metrics.csv NA
6 roh.bed TODO
7 roh_metrics.csv TODO
8 time_metrics.csv NA
9 trimmer_metrics.csv NA
10 wgs_contig_mean_cov.csv NA
11 wgs_coverage_metrics.csv NA
12 wgs_fine_hist.csv NA
13 wgs_hist.csv NA
14 vc_metrics.csv NA
N file description
1 replay.json NA
2 cnv_metrics.csv TODO
3 fastqc_metrics.csv NA
4 fragment_length_hist.csv NA
5 hrdscore.csv TODO
6 mapping_metrics.csv NA
7 ploidy_estimation_metrics.csv NA
8 sv_metrics.csv NA
9 time_metrics.csv NA
10 trimmer_metrics.csv NA
11 wgs_contig_mean_cov_(tumor/normal).csv NA
12 wgs_coverage_metrics_(tumor/normal).csv NA
13 wgs_fine_hist.csv NA
14 wgs_hist.csv NA
15 vc_metrics.csv NA
N file description
1 cancer_report_tables/qc_summary.tsv.gz NA
2 cancer_report_tables/hrd/chord.tsv.gz NA
3 cancer_report_tables/hrd/hrdetect.tsv.gz NA
4 cancer_report_tables/sigs/snv_2015.tsv.gz NA
5 cancer_report_tables/sigs/snv_2020.tsv.gz NA
6 coverage/(tumor/normal).mosdepth.summary.txt NA
7 coverage/(tumor/normal).samtools_stats.txt NA
8 oncoviruses/oncoviral_breakpoints.vcf NA
9 oncoviruses/prioritized_oncoviruses.tsv NA
10 purple/purple.cnv.gene.tsv NA
11 purple/purple.cnv.somatic.tsv NA
12 purple/purple.purity.tsv NA
13 purple/purple.qc NA
14 small_variants/stats/bcftools_stats.txt NA
15 small_variants/stats/pass_bcftools_stats_germline.txt NA
16 small_variants/stats/pass_predispose_bcftools_stats_germline.txt NA
17 small_variants/somatic.pcgr.snvs_indels.tiers.tsv NA
18 small_variants/somatic.pcgr.json.gz NA
19 multiqc_report_data/multiqc_conpair.txt Needed since conpair is not copied over to final dir
N file description
1 pipeline_info/execution_trace.txt NA
2 pipeline_info/software_versions.yml NA
3 amber/amber.homozygousregion.tsv For BAF gaps
4 amber/amber.qc Includes ConsanguinityProportion, Contamination
5 bamtools/wgsmetrics NA
6 chord/chord_prediction.txt NA
7 cuppa/cup.data.csv NA
8 cuppa/cuppa.conclusion.txt NA
9 flagstats/flagstat NA
10 lilac/lilac.candidates.coverage.tsv NA
11 lilac/lilac.qc.tsv NA
12 lilac/lilac.tsv NA
13 orange/orange.json Has majority of columns from WGS results.
14 purple/purple.cnv.gene.tsv NA
15 purple/purple.cnv.somatic.tsv NA
16 purple/purple.purity.tsv NA
17 purple/purple.qc NA
18 sigs/sig.allocation.tsv NA
19 sigs/sig.snv_counts.csv NA
20 virusbreakend/virusbreakend.vcf NA
21 virusbreakend/virusbreakend.vcf.summary.tsv NA
22 virusinterpreter/virus.annotated.tsv NA
N file description
1 pipeline_info/execution_trace.txt NA
2 pipeline_info/software_versions.yml NA
3 cuppa/cup.data.csv NA
4 isofox/isf.summary.csv NA
N file description
1 lilac/lilac.candidates.coverage.tsv NA
2 lilac/lilac.qc.tsv NA
3 lilac/lilac.tsv NA
4 orange/orange.json Has majority of columns from WGS and WTS results.
5 cuppa/cup.data.csv NA
6 cuppa/cuppa.conclusion.txt NA
N file description
1 pipeline_info/execution_trace.txt NA
2 pipeline_info/software_versions.yml NA
3 cancer_report_tables/qc_summary.tsv.gz NA
4 cancer_report_tables/hrd/chord.tsv.gz NA
5 cancer_report_tables/hrd/hrdetect.tsv.gz NA
6 cancer_report_tables/hrd/dragen.tsv.gz NA
7 cancer_report_tables/sigs/snv_2015.tsv.gz NA
8 cancer_report_tables/sigs/snv_2020.tsv.gz NA
9 purple/purple.cnv.gene.tsv NA
10 purple/purple.cnv.somatic.tsv NA
11 purple/purple.purity.tsv NA
12 purple/purple.qc NA
13 smlv_somatic/report/pcgr/pcgr_acmg.grch38.snvs_indels.tiers.tsv NA
14 smlv_somatic/report/pcgr/pcgr_acmg.grch38.json.gz NA
15 smlv_somatic/report/somatic.bcftools_stats.txt NA
16 smlv_somatic/report/somatic.variant_counts_process.json NA
17 smlv_somatic/report/somatic.variant_counts_type.yaml NA
18 smlv_germline/report/germline.bcftools_stats.txt NA
19 smlv_germline/report/germline.variant_counts_type.yaml NA