Sentieon QC

To be run in folder of Sentieon QC outputs together with dedup metrics from Sentieon dedup.

Ouptuts a json with relevant QC-information to whole-genome sequencing or panels(WES included).

WGS

INPUTS

qc_sentieon.pl $id wgs > $id.QC

requires the following parameters from sentieon qc

• --algo MeanQualityByCycle mq_metrics.txt
• --algo QualDistribution qd_metrics.txt
• --algo GCBias --summary gc_summary.txt gc_metrics.txt
• --algo AlignmentStat aln_metrics.txt
• --algo InsertSizeMetricAlgo is_metrics.txt
• --algo WgsMetricsAlgo wgs_metrics.txt

Plus

• --algo Dedup --score_info $scores --metrics dedup_metrics.txt

OUTPUTS

• "ins_size" : "",
• "sd_coverage" : "",
• "dup_reads" : "",
• pct_above_x" : {
  • "80" : "",
  • "20" : "",
  • "5" : "",
  • "10" : "",
  • "15" : "",
  • "25" : "",
  • "40" : "",
  • "60" : "",
  • "30" : "",
  • "1" : "",
  • "90" : "",
  • "50" : "",
  • "70" : "",
  • "100" : ""
• "mapped_reads" : ,
• "num_reads" : "",
• "dup_pct" : "0.",
• "sample_id" : "",
• "mean_coverage" : "",
• "ins_size_dev" : "",
• "median_cov" : ""

Panels

INPUTS

qc_sentieon.pl $id panel > $id.QC

--algo MeanQualityByCycle mq_metrics.txt

• --algo QualDistribution qd_metrics.txt
• --algo GCBias --summary gc_summary.txt gc_metrics.txt
• --algo AlignmentStat aln_metrics.txt
• --algo InsertSizeMetricAlgo is_metrics.txt
• --algo HsMetricAlgo --targets_list $target_intervals --baits_list $target_intervals hs_metrics.txt
• --algo CoverageMetrics --cov_thresh 1 --cov_thresh 10 --cov_thresh 30 --cov_thresh 100 --cov_thresh 250 --cov_thresh 500 cov_metrics.txt

Plus

• --algo Dedup --score_info $scores --metrics dedup_metrics.txt

OUTPUTS

• "sample_id" : "",
• "fold_enrichment" : "",
• "mapped_reads" : "",
• "mean_cov" : ,
• "pct_on_target" : "",
• "ins_size" : "",
• "median_coverage" : "",
• "ins_size_dev" : "",
• "tot_reads" : "",
• "fold_80" : "",
• "dup_pct" : ,
  • "pct_above_x" : {
  • "1000" : ,
  • "100" : ,
  • "1" : ,
  • "10" : ,
  • "30" : ,
  • "500" : ,
  • "250" :
• "dup_reads" : ""