MultiQC_NPM

A MultiQC plugin to support QC efforts within the National Precision Medicine programme in Singapore (NPM), a local initiative that intends to sequence the genomes of 100K individuals (SG100K).

Quick start

Parsing of additional data files through MultiQC_NPM can be enabled using the --enable-npm-plugin option, e.g.:

multiqc . --data-format json --enable-npm-plugin

All other MultiQC options remain unchanged.

Description

MultiQC_NPM builds upon the base functionality of MultiQC to add the following:

• Extended parsing for third-party tools: bcftools gtcheck, picard CollectQualityYieldMetrics, samtools stats FFQ/LFQ.
• Support for custom tools: sg10k-cov-062017.sh, count_variants.py.

For additional context on how each tool is used, please refer to the NPM-sample-qc repository.