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I think that LiftoverVcf isn't working with a gVCF and indel allele in a reference block when trying to left-align indels.
Changing this line to catch if
Hi to all,
I am doing "lift over" from hg19 vcf to hg38 vcf. I use the chain file, obtained from: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1