vcfpolyx counts homopolymer repeats in the wrong position

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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vcfpolyx counts homopolymer repeats in the wrong position #165

Closed ftucos closed 3 years ago

ftucos commented 3 years ago

vcfpolyx is counting homopolymer one base before were the deletion happens. Probably it's not taking into account the left normalization of the VCF file thus reading the first (common) base and not the deleted one. Here an example:

lindenb commented 3 years ago

ah yes, you're right ! I'm gonna fix this.

lindenb commented 3 years ago

I added a +1 when the variant is an indel: https://github.com/lindenb/jvarkit/commit/6d7e78cc303ff2ced435750707c285d169b3fc64

tell me if it fulfills your needs.

ftucos commented 3 years ago

Thank you for the super quick fix. I just tested it and validated a dozen of homopolymers. It's working perfectly! Thank you very much for this useful tool!