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


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.

SNP exome NGS DNA-SEQ • 948 views
Entering edit mode
5.6 years ago
Noushin N ▴ 600

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.


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