This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Cross comparison between Array and NGS data
Dear GATK staff,
I have a 11 samples that were sequenced using NGS (Illumina HiSeq) and 2 of these samples were also genotyped using an Illumina Human Global screening array (Illumina Iscan). I was looking at your latest WDL script and I've noticed a few steps that I think are related but I don't know how to prepare the inputs for them. Any help or additional explanation on them would be really appreciated!
# Check identity of fingerprints across readgroups CrossCheckFingerprints input: haplotype_database_file
What information should I use to create this file? Array data? I have already read these links but I'm still lost:
# Estimate level of cross-sample contamination CheckContamination input: contamination_sites_vcf
What information should I use to create this file?
# Check the sample BAM fingerprint against the sample array CheckFingerprint input: haplotype_database_file input: genotypes
What information should I use to create these files? What does each input stands for?
Thank you very much in advance.