Can I use exome sequencing data from cancer patient's blood to call germline variants?

Question

[ShirleyDai]

Hellos I have some bam files from cancer patients' tumor tissues and blood. The data were originally used for somatic variant calling. But I wonder if I can use the blood data to call germline variants using GATK HC tool. Thanks

[igor]

If you are doing somatic variant calling, you are using a tumor and a normal sample. Normal sample is used for determining germline variants.

[WouterDeCoster]

I don't see any reason why you can't.

[ShirleyDai]

Then if I want to get all SNPs for whole genome, can I do imputation after genotype detection?

[WouterDeCoster]

I've never done anything like that, but I would expect that the SNP data you obtain from WES is insufficient for WGS imputation.

Answer 1

[poisonAlien]

Technically you can. However there is a certain chance that blood cells are contaminated with circulating tumor cells. If you're confident about your normal purity, it shouldn't affect much.

[igor]

Unless you are working with blood cancers, circulating tumor DNA fraction is extremely low.

[ShirleyDai]

Is there a way I can calculate normal purity from BAM files?

[poisonAlien]

I am not sure of methods. But, see below comment by @igor circulating tumor cells are extremely low, so should be okay.