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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.