Jit
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Converting a VCF into a FASTA given some reference !
By Jit 2318 days ago
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)
This script has been modified by others to convert InDels as well, e.g. this by David Eccles
./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl
https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl
