Germline calling with differents sample source

Question

[quentin54520]

Hello all,

I will soon receive new human genome sequencing. Some genomes were made from leukocyte DNA, others from saliva.

I wanted to know if I should take this difference into account and if so when?

For example, I have families for which I have leukocyte DNA for the patient but saliva for the parents.

I saw a publication that made available some sort of reference genome of bacteria present in saliva to act as a decoy at the time of alignment, but other than that I'm not sure how to take it into account.

Thanks for your advices.