I have a few sample vcfs which are not in a very good quality. They are 23andme files from OpenSNP in the following format:
rsID, chromosome no, position, genotype
I have tried remapping them using Galaxy. However, I guess the error is due to the format. The vcfs contain only SNPs.
ANY IDEAS PLEASE? How can i make it work?
These vcfs are mapped on the GRCh36/hg18 and need to be remapped on hg38.
I have a specific list of SNPs (according to the hg38) in a csv format which I need to filter from each of these vcfs after remapping.
Please suggest any alternate workflows if there are any to help me make this work.
I recommend you UCSC Liftover, i tried it and it's working pretty smooth.
https://genome.ucsc.edu/cgi-bin/hgLiftOver
The file you are trying to liftover is not a .vcf.
You need to reorder columns to match the Variant call format, that is #chromosome, #position, #rsID, #refAllele, #altAllele, etc.
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