Frequently Asked Questions (FAQ)

Germline

Germline WGS

Germline Exome

Somatic

Somatic Exome

Question In the somatic_exome.cwl pipeline, what is the difference between interval_list, bait_intervals, target_intervals, per_base_intervals, per_target_intervals, summary_intervals? Or is there documentation somewhere that I can go look at?

Answer bait_intervals and target_intervals together these are the two-tracks of a multi-tracked BED file (although in interval list format). These are use to run CalculateHsMetrics in it's "normal" and familiar mode that results in capture efficiency metrics, on/off target, near target/bait, etc. interval_list is used to limit the variants called by strelka, mutect, pindel, varscan per_base_intervals, per_target_intervals and summary_intervals are inputs to a QC step run for both exome and WGS. This still runs CalculateHsMetrics to generate all three levels of detail, per_base, per_target and summary (summary is basically the same output as the traditional mode but we only allow for one input, not bait and target). With per_base and per_target you would get the additional output file with those respective metrics. A good example is for determining the coverage of ACMG gene exons or ClinVar variants. Since the output contains one line for each ROI provided, you would not want to run either of these on large lists.

Somatic WGS

RNA-seq

WGBS