Incorporate SNP/Indel and generate new sequence from original reference gene sequence

Question

[amar.kant20422]

1. I have SNPs and indel information in the form of SNPs/indel and their position.
2. I have downloaded the sequence of gene from reference genome
3. How to generate the new sequence with incorporated SNP/Indels in the gene sequence of reference?

[liorglic]

Assuming that your SNPs/InDels are in VCF format and use the same coordinates as your genes, this thread could be of help.