How to convert VCF format file into Fasta(.fa) with the Reference data

Question

I need a Software or Python Program for Converting VCF(.vcf) to FASTA(.fa) format with the help of reference (.fa)

Not quite a dupe since it asks for an R or python approach, but very relevant: Converting a VCF into a FASTA given a reference with Python, R. — terdon, Sep 22 '19 at 18:27
https://bioinformatics.stackexchange.com/questions/2825/converting-a-vcf-into-a-fasta-given-a-reference-with-python-r — M__, Sep 23 '19 at 01:46

StupidWolf · Answer 1 · 2019-09-22T20:11:09.713

2

I used FastaAlternateReferenceMaker previously. You will need to download GATK first. Next you prepare your reference genome (reference.fasta) and your vcf file (input.vcf). You will call the GATK function like this:

 java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R reference.fasta \
   -o output.fasta \
   -V input.vcf \

output.fasta will contain the new fasta with snps inserted at sites specific by the vcf file

edited Sep 22 '19 at 20:11

answered Sep 22 '19 at 15:58

StupidWolf

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I got this error when I used gatk on a Linux plaftorm:
A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
– David Enoma May 14 '21 at 11:41
your chromosome names are different – StupidWolf May 14 '21 at 11:50
how do I resolve this please?
Additionally, the vcf files are from somewhere external and I actually subset it to get a specific sample. my reference is https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz
– David Enoma May 14 '21 at 12:13

How to convert VCF format file into Fasta(.fa) with the Reference data

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