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gymrek-lab / TRTools

Toolkit for genome-wide analysis of tandem repeats
https://trtools.readthedocs.io/
MIT License
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mergeSTR can't merge haploid data from HipSTR output #182

Open Lidweixiang opened 1 year ago

Lidweixiang commented 1 year ago

Hi,

Recently I have been processing some haploid vcf files from HipSTR output and I find I can't merge haploid data through mergeSTR, and the errors are as follows:

TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced(line 400 in mergeSTR.py)

I know dumpSTR didn't support haploid, is mergeSTR the same way?

Best, Weixiang

nainai77 commented 1 year ago

I encountered a similar problem when merging the output vcf file of expansionHunter with mergeSTR.

~tr_harmonizer.py", line 209, in InferVCFType raise TypeError('Could not identify the type of this vcf') TypeError: Could not identify the type of this vcf

Have you solved this problem?

Lidweixiang commented 1 year ago

I have no idea about that, do you set the parameter --vcftype to eh ?