QC Workflow Output

The QC workflow --inputdir is a directory of fastq files.

After running the Pipeline the outputdir will have the following output:

• execution_report.html: nextflow execution report
• execution_timeline.html: nextflow timeline
• execution_trace.txt: nextflow trace
• final_bams: for each sample we will have the following files
  • sample_dup_metrics.txt: metrics file
  • sample.sorted.dup.bam: the mapped cleaned and sorted bam file
  • sample.sorted.dup.pf.bam: the final pf bam file
  • sample.sorted.dup.pf.bam.bai: index for pf bam file (this file is need if later running PathWeaver)
  • sample.sorted.dup.pf.bam.csi: index for pf bam file
• final_qc_reports: contains summary report files for all samples
  • Bam_stats_hs_Final.tsv: stats for human bams
  • Bam_stats_pf_Final.tsv: stats for pf bams
  • Bam_stats_total_Final.tsv: stats for both pf and human bams
  • InsertSize_Final.tsv: insert size information for all samples
  • multiqc_report.html: multiqc/fastqc reports for all samples
  • Ratios_hs_pf_reads.tsv: table of ratios of human to pf reads
  • ReadCoverage_final.tsv: table of read coverage for each sample and chromosome
  • run_quality_report.html: a .Rmd script output summarizing run quality
• histograms: for each sample we will have the following files
  • sample_histo.pdf: histogram intermediate file output
• insert_size_metrics: for each sample we will have the following files
  • S3_WGS-batchC_4051126659-ST136_S5.insert2.txt: insert size output
  • S3_WGS-batchC_4051126659-ST136_S5.insert.txt: insert size raw output

GVCF Workflow Output

The GVCF workflow --inputdir is the directory final_bams which is an output of the QC workflow. Most important are the .dup.pf.bam and .dup.pf.bam.csi files.

After running the Pipeline the outputdir will have the following structure:

• chr1: for each sample we will have the following files*
  • sample.chr1.g.vcf
  • sample.chr1.g.vcf.idx
  • sample.chr1_log.txt
• chr11: *
• chr12: *
• chr13: *
• chr14: *
• chr2: *
• chr3: *
• chr4: *
• chr5: *
• chr6: *
• chr7: *
• chr8: *
• chr9: *
• chr14: *
• execution_report.html: nextflow execution report
• execution_timeline.html: nextflow timeline
• execution_trace.txt: nextflow trace