multiple alleles for a diploid genome?

[caswater]

When analyzing a diploid genome, GATK genotyper complains about multiple alleles found in a region, the message is shown below,...

"WARN 13:57:25,771 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at chr1:19203155 has 4 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument"

As it is an diploid genome, how come 4 different alleles could be found? a bit confused here.

Thanks a lot for your kind advice on this

[swbarnes2]

When analyzing a diploid genome, GATK genotyper complains about multiple alleles found in a region, the message is shown below,...

"WARN 13:57:25,771 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at chr1:19203155 has 4 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument"

As it is an diploid genome, how come 4 different alleles could be found? a bit confused here.

Thanks a lot for your kind advice on this

Your samples might not be pure. Or you might have alignment errors. Or your raw data ahs errors (like homopolymer mistakes).

Probably, it's an area where the alignment is poor.

[caswater]

Thanks a lot for your advice. I just checked the files, and those regions were indels, and they seemed to be short repetitive sequence stretches (just around ~5bp something). I guess it is likely alignment problems. Will check SNPs and see if there is anything wrong with it.

by the way, if we see multiple alleles along a chromosome, will it indicate something like polysomy for the individual? how can we detect polysomic region then?

Thanks again for your advice

Best

[ymc]

It can be polysomy. Or a particular region is duplicated couple times relative to the reference genome