Hi,
First please make sure you use the most recent version. If the problem persists, please provide a few lines of you VCF file to help trouble shooting. Thanks
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Hi,
First please make sure you use the most recent version. If the problem persists, please provide a few lines of you VCF file to help trouble shooting. Thanks
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:
Output:
Expected output: