Hello, I have a file which gives me the position of the altered nucleotide or small insertion or deletion (reference allele and altered allele). Is there any tool which can be used to perform these changes on the reference nucleotide sequence and incorporate the ALT_ALLELE changes ?

    CHROM	POS	REF_ALLELE	ALT_ALLELE	TRANSCRIPT_ID	GENE_ID	GENE_NAME	REGION	VARIANT_TYPE	REF_AMINO	ALT_AMINO	AMINO_POS	SIFT_SCORE	SIFT_MEDIAN	NUM_SEQS	dbSNP	SIFT_PREDICTION
    SL3.0ch00	723860	A	C	mRNA.Solyc00g005060.1.1	gene.Solyc00g005060.1	Solyc00g005060.1	CDS	NONSYNONYMOUS	W	G	52	0	4.32	1	novel	DELETERIOUS (*WARNING! Low confidence)
    SL3.0ch00	723867	A	C	mRNA.Solyc00g005060.1.1	gene.Solyc00g005060.1	Solyc00g005060.1	CDS	SYNONYMOUS	G	G	49	1	4.32	1	novel	TOLERATED
    SL3.0ch00	723903	T	C	mRNA.Solyc00g005060.1.1	gene.Solyc00g005060.1	Solyc00g005060.1	CDS	SYNONYMOUS	G	G	37	1	4.32	1	novel	TOLERATED


Give `bcftools consensus` a try

https://samtools.github.io/bcftools/bcftools.html#consensus

or GATK's `FastaAlternateReferenceMaker` (slower than bcftools consensus)

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php