Question: how to merge individual vcf to reference genome using python script.
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gravatar for ahmadpir40
3 months ago by
ahmadpir400
ahmadpir400 wrote:

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.

ADD COMMENTlink modified 3 months ago by Amar640 • written 3 months ago by ahmadpir400
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gravatar for Amar
3 months ago by
Amar640
Amar640 wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Amar640

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

ADD REPLYlink written 3 months ago by ahmadpir400
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