References

ICGC ARGO

dnaalnqc: https://github.com/icgc-argo-workflows/dnaalnqc

vcfqc: https://github.com/icgc-argo-workflows/vcfqc

DRAGEN

Illumina DRAGEN Bio-IT Platform 3.7 User Guide

Bedtools subtract

https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html

NPM-sample-qc

https://github.com/c-BIG/NPM-sample-qc

Samtools stats

http://www.htslib.org/doc/samtools-stats.html

Samtools view

http://www.htslib.org/doc/samtools-view.html

VCF Format

[https://samtools.github.io/hts-specs/VCFv4.2.pdf]

VerifyBamID2

https://github.com/Griffan/VerifyBamID

VerifyBamID reference panel

Pre-calculated reference panel of 1000 Genome Project phase 3 dataset: 100,000 sites mapped on GRCh38