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change the columns of vcf file

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?

snp
• 1,942 views • link
updated by Biostar Biostar • written by GK1610 GK1610

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.
• 1 views • link
written by Ram Ram

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

• 1 views • link
written by finswimmer finswimmer

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