Question: Remapping genomic coordinates to account for indels
gravatar for jergosh
3.9 years ago by
United Kingdom
jergosh60 wrote:

I'm interested in obtaining coding sequences of my favourite gene in all individuals from the 1000 genomes project (and similar endeavours). I use GATK to get the right subset of variants, vcf-consensus to map these variants onto the reference genome and finally samtools to extract the individual exons. This works fine if the variants are SNPs but if there are any indels, this changes the coordinates of exons and I end up getting the wrong region. Is there any generic way of remapping genomic coordinates to account for the changes created by indels?

vcftools gatk vcf • 1.1k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by jergosh60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1468 users visited in the last hour