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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Variant Calling in Low-Complexity Regions #222

Closed zhoudreames closed 2 years ago

zhoudreames commented 2 years ago

there are some variants where located in Low-Complexity Regions can not be identified by using octopus software. how to solve it ？ thanks ~ image

aquaskyline commented 2 years ago

What's the truth variant at the position?

zhoudreames commented 2 years ago

What's the truth variant at the position?

yes ,this variants were support by hifi data.

zhoudreames commented 2 years ago

I using many Illumina variants caller can not identity such variants ，whether those variations located in such areas themselves are difficult to detect ？and is there any way to deal with it ？

dancooke commented 2 years ago

Looks like all reads spanning this locus have mapping quality 0, so there is at least one other location where they map equally well. I'm not aware of any mapping-based variant caller that will attempt to use MQ0 reads (by default). If you really want to call this region then you can add the options --min-mapping-quality 0 --dont-model-mapping-quality, but don't expect reliable calls.

zhoudreames commented 2 years ago

Looks like all reads spanning this locus have mapping quality 0, so there is at least one other location where they map equally well. I'm not aware of any mapping-based variant caller that will attempt to use MQ0 reads (by default). If you really want to call this region then you can add the options --min-mapping-quality 0 --dont-model-mapping-quality, but don't expect reliable calls.

thanks~