Liftover vcf file from hs37d5 assembly to b37 assembly

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Hello,

I have a vcf file which consists of mutations that was generated using the GATK variant calling workflow. For this the hs37d5 assembly was used.
The problem is, that all GAKT reference resources use the b37 assembly, and if I simply use them, my script fails, because for some variants (less than 0.1%) there is a mismatch between the b37 and hs37d5 reference genome.
So my idea was to simply remap the variants of the VCF file to b37. I planed on using something like CrossMap, but no chain files are available for my reference assemblies.

Does anyone have an idea how I can remap the variants from my hs37d5 vcf file to the b37 assembly without the use of chain files, or any other suggestions?

I would greatly appreciate them!

Cheers


vcf


liftover


assembly

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