how to merge individual vcf to reference genome using python script.

Question

[ahmadpir40]

I need python script to merge the Individual vcf to reference genome to get a new reference. Any suggestion about it how to write it.

Answer 1

[Mark]

Super relevant biostars thread that answers this question: New Fasta Sequence From Reference Fasta And Variant Calls File?

Actual answer: Why reinvent the wheel when someone has done the hard work for you? FastaAlternateReferenceMaker is part of GATK, there's vcf-consensus in vcftools, lots of options.

[ahmadpir40]

Dear Amar thanks for response. i hope it will help.