How to convert a VCF into a FASTA given a reference with Python?

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Abhijeet Singh

https://www.biostars.org/p/360900/

Oscar Gabriel Beltran

https://github.com/rlebron88/vcf2fasta

Mohamed Belhocine

Abhijeet Singh & Oscar Gabriel Beltran Thank you for your answers

I tried the 2 methods but finally, I used GATK :

java -Xmx5g -jar /apps/gatk/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R input.fasta --variant var.vcf.gz -o output.fasta

Marwan Mahmood Saleh

Mohamed Belhocine Can I convert Whole genome sequence?