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paulhager / smart-phase

A comprehensive and intelligent clinical phasing tool
GNU General Public License v3.0
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Impossible to open VCF v4.2 files.. #10

Closed fpichon closed 3 years ago

fpichon commented 3 years ago

Hi, thanks for your tool, seems useful. However, I could not open any VCF file... Have the following error: Exception in thread "main" java.lang.Exception: While parsing filtered variants, tried to split using '\t' but failed. Please ensure your file is tab-seperated, or ends in .csv if it is comma separated. at smartPhase.FilteredVariantReader.<init>(FilteredVariantReader.java:94)

My VCF is generated by GATK and the version is: ##fileformat=VCFv4.2 Thanks for your help.

timjeske commented 3 years ago

Dear fpichon,

thank you for your interest in our tool!

I guess, the error message is due to the fact that you didn't provide a gene region BED file. SmartPhase does generally not phase all variants within the filtered variants file. Either it generates all pairs of variants in defined gene regions (option -g) or you directly provide preselected pairs. As it seems you did not provide a gene region file, SmartPhase assumes that you provide preselected pairs in a tab separated file causing this error message. You can check our use case to see how it works here.

I hope I could help. Let us know if you still run into problems!

Best regards Tim