Closed fpichon closed 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
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.