Consensus for haploid genome from vcf file

Question

[indranipoddar]

Hello,

I am trying to create a consensus from ref & vcf file for haploid genome. And I know about vcf-consensus but I want to create consensus for a region in that haploid genome with vcf. I see vcftools have examples like chr:start-end for region extraction then vcf-consensus but as because it is haploid , I can't use that same format.

I will highly appreciate any suggestions.

Thanks in advance.

Answer 1

[GouthamAtla]

GATK's FastaAlternateReferenceMaker takes a <fasta file>, a <VCF file> and an [interval file] and gives you the new fasta by incorporating the SNPs from VCF file.

[indranipoddar]

Thank you so much for your reply. I will try to use this but do you know if there is any web version of this module.

If not then I can download GATK.

Thank you again.

[GouthamAtla]

As far as I know...you have to download it and use.