Theoretical genome sequence

Question

[skdutta2091]

Can anybody please help me in the construction of theoretical genome sequence? Actually I am having the SNP and InDel data and the reference genome. So is there any possibility of constructing a theoretical genome sequence using the SNP and InDel data just by substituting/inserting/deleting these variants in the reference genome at the exact positions?

It will be a great help to get any kind of reply or ideas...

Answer 1

[GouthamAtla]

FastaAlternateReferenceMaker

Answer 2

[Len Trigg]

FastaAlternateReferenceMaker looks like it may be a simple way if you have variant sites and the goal is to make a new (haploid) reference that incorporates those variants.

If, on the other hand you are trying to reconstruct the (potentially diploid) genome of an individual (i.e. you actually have genotypes rather than just a list of variant sites and alleles), then you can use the rtg samplereplay command from RTG Core to generate the genome corresponding to a sample contained in a VCF. For diploid chromosomes you will get two copies of each chromosome output. (You can also use samplereplay to generate a haploid alternate reference by representing your input data as a haploid sample containing all the variants, although there is not currently the option to output heterozygous SNPs with IUPAC ambiguity codes).