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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Remove field shadowing superclass field #137

Closed Lenbok closed 2 years ago

Lenbok commented 2 years ago

I was wondering why ExpansionHunter was sometimes not producing results in some relatively low coverage situations and went looking to see if there were any coverage thresholds hardwired.

I found out about the (undocumented) MinimalLocusCoverage parameter and went to try it. However it had no effect in my examples - only the default threshold of 10 was ever being applied. I tracked the problem down to the fact that RepeatAnalyzer inadvertently contains a field that shadows that of the superclass. Removing that allows the locus-specific coverage thresholds to work.

hchetia commented 2 years ago

Hi @egor-dolzhenko @Lenbok I have been trying the same thing. Could you please share what changes you made and to which script in the source directory?

Lenbok commented 2 years ago

You just add a MinimalLocusCoverage line into the variant catalog entry for the variant of interest (I don't think you can do it for all). The default is 10, in my case I have set it to 1. e.g.:

...
{
    "LocusId": "DMPK",
    "LocusStructure": "(CAG)*",
    "MinimalLocusCoverage": 1,
    "ReferenceRegion": "19:46273462-46273522",
    "VariantType": "Repeat"
}
...
hchetia commented 2 years ago

Thanks @Lenbok . Do you mean that this solution didn't work for all the loci in the EXPHUNTER catalog?

Lenbok commented 2 years ago

As far as I can tell, you would need to add that parameter to every entry in the catalog.

egor-dolzhenko commented 2 years ago

@Lenbok @hchetia By next week we'll add a parameter that would allow setting MinimalLocusCoverage for all repeats from the command line.