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
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!