change the columns of vcf file

Question

[GK1610]

I have a genotype hg19_vcf file of 100 individuals with hg19 coordinates.

I pull out chromosome, position and rsids from vcf file and use NCBI remap service to convert the coordinates of vcf file to hg38.

How do I combine the new coordinates with genotypes information from hg19_vcf file?

[Ram]

What have you tried? You have a good grasp on the individual steps, so finding tools for each step should be straightforward.

You wish to

1. extract specific attributes from a VCF file,
2. run a service on a subset of elements from the extracted dataset to create a new mapping dataset; and
3. create your output dataset with the service output combined with a few attributes from the extracted dataset using the mapping dataset.

[finswimmer]

Hello,

you can choose that the output of the remap service is again a vcf file. So there should be no need to combine anything. Just give in your vcf you like to liftover and get back the lifted over one.

fin swimmer