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jbelyeu / unfazed

Unfazed by genomic variant phasing
MIT License
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no usable informative sites #3

Open WouterSteyaert opened 2 months ago

WouterSteyaert commented 2 months ago

Dear Jonathan,

When I try running unfazed I always get the notion that there are no usable informative sites, for any input variant. I am wondering if genomes are supported for which the chromosome names start with 'chr', because in the screenoutput it says that there are no intervals for 1:16080000-16090000 (for example) while all my input files are 'chr' based. Do you have an idea why that is?

Best wishes, Wouter

WouterSteyaert commented 2 months ago

OK. I spotted the problem. my VCF starts with some 'unconventional chromosome' not starting with 'chr' and thus the function 'get_prefix' results in an empty prefix causing the issues. I will filter the VCF beforehand and let you know the result