I'm interested in obtaining coding sequences of my favourite gene in all individuals from the 1000Genomes (and similar projects). 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?
Remapping genomic coordinates to account for indels
variants;structural variation
I think that you need a LiftOver Chain file to transform your coordinates. You can obtain such a file using bcftools consensus with the -c parameter:-c, --chain <file>         write a chain file for liftoverThen you can use it to transform coordinates in various genomic formats using CrossMap.