Is it possible to check whether a sample is progeny of the other two samples from exome sequenced data?

Question

[bioinforesearchquestions]

Hi,

I have exome sequenced reads from four samples. There is a sample mix-up. I have been asked to help on this issue.

SampleA, SampleB, SampleC, SampleD

What I really need to know is whether sampleA is the progeny of sampleB and sampleC?

I generated the FASTQ files, BAM and variant calling files.

Answer 1

[Noushin N]

I do not know if there are established tools for this purpose; but I think one should be answer this relatively easily given the data you mentioned. Assuming that you are looking at human genomes, you can compare the genotypes across a set of common polymorphisms (e.g. common SNPs from dbSNP).

If sample A is a progeny of sample B, sample A will have to be homozygous or heterozygous alternate in the great majority (excluding sequencing errors / do novo mutations) of loci where sample B is homozygous alternate. Similarly, sample A cannot be homozygous alternate in loci where sample B is homozygous reference.