any tools for updating reference sequence file to include the variants from the vcf file?

Question

[mheyda]

Hi,

Does anyone know any tool which can retrieve or build the most possible (statistically the best one or the closest on to the original) sequence based on variant calling file (vcf file). In other word I have the closest genome to the fastq read file and I did variant calling so I have the vcf file, but I want to change this genome file according to the vcf file to contains all those variants

Thanks for your help in advance

Answer 1

[Pierre Lindenbaum]

FastaAlternateReferenceMaker https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php

[mheyda]

Thanks , Do you know what is this input.intervals?