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bioinformatics-centre / BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers
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Genotyping for the inversions #39

Open shehongbing opened 2 years ago

shehongbing commented 2 years ago

Hi, it's a powerful tool I used. So could the tool genotype for the inversions?

jonassibbesen commented 2 years ago

Yes, if you have a set of candidate inversions, BayesTyper should be able to genotype those.

shehongbing commented 2 years ago

Hi, I have another question. I want to genotype population on custom VCF file.

As for the insertion or deletion, it is easy to generate the VCF. A deletion is as an example.

CHROM POS ID REF ALT QUAL FILTER INFO

chr4 106924192 . TGCCCAGGAAATTGAAG T . . .

it means a deletion occur in query.

However, what about the inversion. For example, there is a inversion between ref and query.

ref, start - end (10 -20) VS. query, start - end (20 - 30). Which is the correct format as follows:

(1)

CHROM POS ID REF ALT QUAL FILTER INFO

chr4 10 . AAGGCCTTCC AAGGCCTTCC . . .

or (2)

CHROM POS ID REF ALT QUAL FILTER INFO

chr4 10 . AAGGCCTTCC CCTTCCGGAA . . .

Thx