I would like to perform an all VS all contamination check for about two dozen human tumor samples.
I would like to have an estimate/metric for every sample in the set if there is any other sample in the set a contamination donor.
Is there any method available which targets exactly this application?
I do not care if the method requires any SNP calls beforehand or if it uses a kmer method or whatever.
It is also OK, if I can estimate the baseline of the metric beforehand and then double check samples which overshoot in the metric which is provided by the tool.
EDIT: My samples are Illumina NGS samples. It is from a large panel. But methods working on WES or WGS are also welcome, because the panel covers quite a bit of the genome. Coverage is super high. 500x at minimum. The donors of the samples are not directly genetically related, so we expect quite some diversity in terms of SNPs.
You really need to give details on the specimen. I assume we talk some NGS here, but how would we know?