simplex-metrics

Category: POST-CONSENSUS

Collect QC metrics for simplex sequencing data

Description

Collects a suite of metrics to QC simplex sequencing data.

Inputs

The input to this tool must be a BAM file that is either:

1. The exact BAM output by the group tool (in the sort-order it was produced in)
2. A BAM file that has MI tags present on all reads (usually set by group and has been sorted into template-coordinate order

Calculation of metrics may be restricted to a set of regions using the --intervals parameter. This can significantly affect results as off-target reads often have very different properties than on-target reads due to the lack of enrichment.

Outputs

The following output files are produced:

1. <output>.family_sizes.txt: metrics on the frequency of CS and SS families of different sizes
2. <output>.simplex_yield_metrics.txt: summary QC metrics produced using 5%, 10%, 15%…100% of the data
3. <output>.umi_counts.txt: metrics on the frequency of observations of UMIs within reads and tag families
4. <output>.simplex_qc.pdf: (optional) a series of plots generated from the preceding metrics files for visualization. This file is only produced if R is available with the required packages (ggplot2 and scales). Use --description to customize plot titles.

Within the metrics files the prefixes CS and SS are used to mean:

• CS: tag families where membership is defined solely on matching genome coordinates and strand
• SS: single-stranded tag families where membership is defined by genome coordinates, strand and UMI

Arguments