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aehrc / VariantSpark

machine learning for genomic variants
http://bioinformatics.csiro.au/variantspark
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VariantSpark Hail Interface #96

Open ArashBayatDev opened 5 years ago

ArashBayatDev commented 5 years ago

When using VariantSpark interface for Hail to run important analysis, VariantSpark expect to have exactly one allele in REF and ALT field. If there was any issue (some dataset have . in the ALT field) the process fails but it does not report which variant causing the error. So it is difficult for user to Understand and fix the problem.

I suggest to report the offending line when loading data fails to complete.

rocreguant commented 9 months ago

Will implement a warning if the VCF is not bi-allelic.