Matthieu

I have a similar issue in v0.3.3, where the ref allele is indeed the reverse complement but not the alt allele. command: CrossMap.py vcf chain/hg19ToHg38.over.chain.gz test.3.vcf genomes/Hsapiens/hg38/seq/hg38.fa test.3.hg38.vcf Input: ##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ALS 15 23102357 . C A . . . GT 0/1 Output: ##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ALS 15 22770732 . G A . . . GT 0/1 Expected output: ##fileformat=VCFv4.2 #CHROM POS ID REF...