This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Whole genome genotyping

Hello,

I am trying to do whole genome (or a subset) genotyping for an individual in order to find out the heterozygous loci.

I know genotyping is typically only done for sites where a variation is discovered, but in my case, the individual is the reference individual so it has no difference to itself. I was wondering if there is any genotyping tool that does not involve variant calling?

I have the genome assembly for the individual.

Any help would be greatly appreciated!

Zoe

genotyping ngs
• 212 views • link
updated by colindaven colindaven • written by zpl015 • zpl015

1 answer

It could be I am misunderstanding your intention, and you do not provide full information (human data?), but if you have a genome assembly can't you just map the reads back to the genome assembly and call SNVs and thus heterozygous sites ? Of course, you'll see problems with reference bias and mapping problems depending on how good the genome assembly is, but it's a step in the right direction.

• 0 views • link
written by colindaven colindaven

Thanks for your answer! It's bird genome data. This bird was sequenced with a high depth (~100x), and its genome assembly is used as the reference genome for the rest of the population. However, I am not interested in the rest of the population but just the reference bird itself (I have the raw data and the genome assembly of the reference bird). Maybe I got you wrong, I am not sure what is the point mapping the sequence reads of the individual to it's own genome assembly?

• 0 views • link
written by zpl015 • zpl015

Log in to answer this question.

More posts like this