VCF failed liftover, incorrect alternate allele

Question

[musaevdamir]

Hi all,

I lifted over hg38 vcf to hg19 one. However, some positions were corrupted - for some genes hg38 had sense strand while hg19 had anti-sense strand. So, after liftover the reference base was changed (e.g. if in chr1:12345 you had base A in hg38, it changed to T in hg19), but the alternate allele was not changed accordingly (e.g. if the alternate allele was C in hg38, it stayed C in hg19 instead of being changed to G).

The command below was run:

python CrossMap.py vcf /chain_file/hg38ToHg19.over.chain /projects2/vcfs/Mito_4208hg38.vcf /projects/human_reference/ucsc.hg19.fasta /projects2/vcfs/Mito_4208Hg19.vcf

Do you guys know what might have gone wrong?

Thanks, Damir