Hello!
I would like to provide BAM files consisting of aligned simulated genomic data to one specific model to conduct a small experiment relevant to demographic analysis
To do so, I need to simulate some reads for more than one individual. However, it's important not to make it completely random, since those individuals should belong to one population. Could you give examples of simulation tools that can do such trick?
Thank you guys in advance
•
written
by
all.lirik •
A simple, but not so efficient approach would be to generate a genome for each individual, put those genomes into a single FASTA file then generate reads from all the genomes.
You could generate genomes with
https://github.com/yjx1217/simuG
or by applying a VCF file to an existing genome. For large genomes and large populations, the process could be prohibitively inefficient.
Alternatively, you may look for existing software tools like this GenomePop:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-223
Thank you! I'll definitely look through those.
Actually, I found exactly what I needed in ATLAS
It does have some limitations (simulates it's own reference, rather than using the real one as input), but it's still useful for me
sounds good, thanks for following up with an interesting solution
Log in to answer this question.
