How to identify whether the sample is from only one person and whether the sample is tumor or normal

Question

[tan]

How to obtain this information only through fastq data

Answer 1

[Cyriac Kandoth]

Is this a tricky bonus question from a teacher? :) Happy to oblige.

Assuming it's DNA data, align and perform germline variant calling to generate a gVCF. Then use tools like Contest that can check for cross-sample contamination. Basically they're looking for lots of heterozygous SNPs that deviate from the expected 50:50 read support. Or an enrichment of triallelic sites which can only happen when two or more people's DNA got mixed up.

To figure out whether it's a tumor, you can run a CNV caller - most tumors have some degree of aneuploidy i.e. segments of the genome that are not diploid. And/or look for the very recurrent oncogenic hotspots like KRAS G12 or TP53 LoF mutations.