VCF to Fasta with out reference
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16 months ago
the_cowa ▴ 40

Hi,

I have a vcf file which contains multiple CDS from a mrna, I just need to convert that vcf to fasta with alt allele for het and hom sites(consensus). Yeah normally we will do with this bed tools and FastaAlternateReferenceMaker, but my question is with out an reference fasta is this possible to do the same?

vcf gatk • 427 views
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how would you know what is in between the variants if you don't use reference sequence?

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