I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to convert this VCF data into FASTA format?
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$\begingroup$ What is "MyGenome" exactly? Will they sequence your entire genome? Only your exome? Specific regions of the exome? $\endgroup$– terdon ♦Feb 27, 2018 at 16:35
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$\begingroup$ @terdon Whole genome 30X on HiseqX. Link $\endgroup$– bennFeb 27, 2018 at 16:39
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$\begingroup$ Yeah, that doesn't sound like actual whole genome. Or, rather, it sounds like they might sequence the whole genome but then only analyze specific regions of it (which is a reasonable thing to do, I'm not saying they're swindling you). "myGenome is a whole genome screening test [. . . ]". If so, the method in b.nota's answer won't accurately reconstruct your genome, but only those regions of your genome that differ from the reference genome in the regions they happened t screen. $\endgroup$– terdon ♦Feb 27, 2018 at 16:42
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$\begingroup$ @terdon depends a bit on how they make the VCF file, don't you think? The interpretation is only based on specific regions, but they should have a file with all variants which OP should get for this VCF -> FASTA exercise. $\endgroup$– bennFeb 27, 2018 at 16:58
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2$\begingroup$ Possible duplicate of How to manipulate a reference FASTA or bam to include variants from a VCF? $\endgroup$– gringer ♦Feb 27, 2018 at 20:32
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1 Answer
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You can try gatk function FastaAlternateReferenceMaker
java -jar GenomeAnalysisTK.jar \
-T FastaAlternateReferenceMaker \
-R reference.fasta \
-o output.fasta \
-L input.intervals \
-V input.vcf \
[--snpmask mask.vcf]
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1$\begingroup$ It might be worth pointing out that this will only reconstruct the OP's genome if the OP has WGS data. If not, I this tool will presumably use the reference genome for everything not explicitly mentioned in the file, so it won't be the OP's genome, per se. $\endgroup$– terdon ♦Feb 27, 2018 at 16:36
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$\begingroup$ @b.nota thank you for your answer. Just want to let you know that I've contacted veritas support for more information (still awaiting their response) and will accept your answer once I'm able to confirm that this works. $\endgroup$ Mar 8, 2018 at 13:35